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Performance issues in OpenClinica 3.1.2

24

Comments

  • ccollinsccollins Posts: 378 admin
    Hi Gerben, Cuneyt,
    We are looking into what's happening. Any further detail you can provide on when this happens would be helpful (which URLs, the size of your database, your CRFs and rules, one user or multiple).
    Thanks,
    Cal
    -----Original Message-----
    Sent: Tuesday, January 31, 2012 7:43 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben,
    Thanks for your input.
    My postgres uses the defaults (I didn't change anything and followed
    the OC installation guide).
    During the upgrade I also followed the instructions provided by OC
    upgrade manual.
    Where are the "performance scripts"?
    How do you "REINDEX"?
    How do you change memory settings for postgress?
    Thanks,
    Cuneyt.
    PS: This is only happening in version 3.1.2. So it is not something
    that gradually happened, thats why I didn't suspect the database
    indexes.
    On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    > > Hello Cuneyt,
    > >
    > > Just to get the picture clearer:
    > > - did you run the performance scripts that created the extra indexes
    > > successfully?
    > > - how often do you do a REINDEX?
    > > - did you finetune your memorysettings for postgres?
    > >
    > > Kind regards,
    > >
    > > Gerben Rienk
    > >
    >> >> Hi Michael,
    >> >> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >> >> for the information.
    >> >> I agree with Doug that this is a software issue. It looks like it is
    >> >> introduced in 3.1.2.
    >> >> I would also like to know what the OC project managers (Tom, Ben)
    >> >> think about this and what is their suggestion; that is, waiting for a
    >> >> software patch or upgrading the hardware to SSD's?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >> >> wrote:
    >>> >>> Hi Doug,
    >>> >>>
    >>> >>> Although I agree with you I do not have possibilities to do anything
    >>> >>> software wise!
    >>> >>>
    >>> >>> Regards
    >>> >>>
    >>> >>> Krister
    >>> >>>
    >>> >>> -----Original Message-----
    >>> >>>
    >>> >>> [mailto:[email protected]]
    >>> >>> On Behalf Of Douglas Bain
    >>> >>> Sent: 30 January 2012 17:54
    >>> >>> To: [email protected]
    >>> >>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>> >>>
    >>> >>> I would suggest looking more closely at the software than the hardware.
    >>> >>> Throwing fast hardware at the problem is a workaround, but not the
    >>> >>> solution.
    >>> >>> Typically an eCrf page submit or retrieval only effects a very small
    >>> >>> volume
    >>> >>> of data. A single subjects data may only be 5k. Waiting to read this off
    >>> >>> disks following disk index reads will always be slow in comparison to an
    >>> >>> in
    >>> >>> memory operation. Running sequential rules demands pre SQL
    >>> >>> optimisation.
    >>> >>>
    >>> >>> Doug Bain
    >>> >>>
    >>> >>>
    >>> >>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>> >>> wrote:
    >>> >>>
    >>>> >>>> Dear Krister,
    >>>> >>>>
    >>>> >>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on the
    >>> >>> Performance page in the OpenClinica Wikibook, thinking they would
    >>> >>> dramatically speed up OpenClinica, and your story provides further
    >>> >>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>> >>> disks
    >>> >>> that use SSDs):
    >>>> >>>>
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>> >>>> "Disk requirements: Whilst the space taken up for the application and
    >>> >>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>> >>> faster
    >>> >>> disks, including SSDs (solid state disks) and high speed hard disks,
    >>> >>> will
    >>> >>> speed up the response times of PostgreSQL or Oracle. For example,
    >>> >>> OpenClinica Optimized(tm) Hosting (Clinical Trials in the Cloud) uses
    >>> >>> Fusion-io's hybrid disk technology to improve database performance.
    >>> >>> Additionally, one user reported faster performance on the OpenClinica
    >>> >>> user
    >>> >>> list."
    >>>> >>>>
    >>>> >>>> If others are thinking about using SSDs, they should be aware that,
    >>>> >>>> just
    >>> >>> like regular hard drives, SSDs do fail
    >>> >>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,2923.html)
    >>> >>> , and should be backed up regularly and use RAID where appropriate (as
    >>> >>> with
    >>> >>> regular hard drives).
    >>>> >>>>
    >>>> >>>> May and Cuneyt, were your versions of OpenClinica upgrades, or fresh
    >>> >>> installs? There was a fix for 404's and some consolidation of CSS that
    >>> >>> should have sped up 3.1.2 a little (mentioned on
    >>> >>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>> >>>>
    >>>> >>>> Yours,
    >>>> >>>>
    >>>> >>>> Michael
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>> >>> On Behalf Of Krister Kristianson
    >>>> >>>> Sent: 30 January 2012 13:40
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> A trick that I been very successful with is to put the database on a
    >>>> >>>> SSD
    >>> >>> drive. What took up to 10 seconds now takes less than 1 second using
    >>> >>> 3.1.2
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Xi, Xuemei
    >>>> >>>> Sent: 30 January 2012 14:29
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2 is
    >>> >>> slower to load the page than OC3.1.1
    >>>> >>>>
    >>>> >>>> Thanks
    >>>> >>>> May
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Cuneyt Parlayan
    >>>> >>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> Hi all,
    >>>> >>>>
    >>>> >>>> We are having some performance problems in 3.1.2 which was not the case
    >>>> >>>> in
    >>> >>> earlier versions.
    >>>> >>>>
    >>>> >>>> When data is entered, it takes ± 5 seconds to open the window and
    >>> >>> another
    >>>> >>>> 5 seconds to save the data.
    >>>> >>>> This was not the case before.
    >>>> >>>> Anyone else experiencing this?
    >>>> >>>> Thanks, Cuneyt.
    >>>> >>>>
    >>>> >>>> --
    >>>> >>>> Cuneyt Parlayan
    >>>> >>>>
    >>>> >>>> Datamanager
    >>>> >>>> Department of Pathology
    >>>> >>>> VU University Medical Center
    >>>> >>>> Amsterdam - The Netherlands
    >>>> >>>>
  • mx8866mx8866 Posts: 109
    I notice OC3.1.2 Performance issue relates to the rules and simple conditions. I am developing some CRF, no real data. When I load the initial CRF with 6 to 10 hilde/show conditions, it loads the page slow.
    When I save the testing data which will trigger the rules, it will save very slow and load the page.
    Best Regards,
    May
    -----Original Message-----
    Sent: Tuesday, January 31, 2012 7:31 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben, Cuneyt,
    We are looking into what's happening. Any further detail you can provide on when this happens would be helpful (which URLs, the size of your database, your CRFs and rules, one user or multiple).
    Thanks,
    Cal
    -----Original Message-----
    Sent: Tuesday, January 31, 2012 7:43 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben,
    Thanks for your input.
    My postgres uses the defaults (I didn't change anything and followed the OC installation guide).
    During the upgrade I also followed the instructions provided by OC upgrade manual.
    Where are the "performance scripts"?
    How do you "REINDEX"?
    How do you change memory settings for postgress?
    Thanks,
    Cuneyt.
    PS: This is only happening in version 3.1.2. So it is not something that gradually happened, thats why I didn't suspect the database indexes.
    On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    > > Hello Cuneyt,
    > >
    > > Just to get the picture clearer:
    > > - did you run the performance scripts that created the extra indexes
    > > successfully?
    > > - how often do you do a REINDEX?
    > > - did you finetune your memorysettings for postgres?
    > >
    > > Kind regards,
    > >
    > > Gerben Rienk
    > >
    >> >> Hi Michael,
    >> >> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >> >> for the information.
    >> >> I agree with Doug that this is a software issue. It looks like it is
    >> >> introduced in 3.1.2.
    >> >> I would also like to know what the OC project managers (Tom, Ben)
    >> >> think about this and what is their suggestion; that is, waiting for a
    >> >> software patch or upgrading the hardware to SSD's?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >> >> wrote:
    >>> >>> Hi Doug,
    >>> >>>
    >>> >>> Although I agree with you I do not have possibilities to do anything
    >>> >>> software wise!
    >>> >>>
    >>> >>> Regards
    >>> >>>
    >>> >>> Krister
    >>> >>>
    >>> >>> -----Original Message-----
    >>> >>>
    >>> >>> [mailto:[email protected]]
    >>> >>> On Behalf Of Douglas Bain
    >>> >>> Sent: 30 January 2012 17:54
    >>> >>> To: [email protected]
    >>> >>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>> >>>
    >>> >>> I would suggest looking more closely at the software than the hardware.
    >>> >>> Throwing fast hardware at the problem is a workaround, but not the
    >>> >>> solution.
    >>> >>> Typically an eCrf page submit or retrieval only effects a very small
    >>> >>> volume of data. A single subjects data may only be 5k. Waiting to
    >>> >>> read this off disks following disk index reads will always be slow
    >>> >>> in comparison to an in memory operation. Running sequential rules
    >>> >>> demands pre SQL optimisation.
    >>> >>>
    >>> >>> Doug Bain
    >>> >>>
    >>> >>>
    >>> >>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>> >>> wrote:
    >>> >>>
    >>>> >>>> Dear Krister,
    >>>> >>>>
    >>>> >>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >>>> >>>> the
    >>> >>> Performance page in the OpenClinica Wikibook, thinking they would
    >>> >>> dramatically speed up OpenClinica, and your story provides further
    >>> >>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>> >>> disks that use SSDs):
    >>>> >>>>
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>> >>>> "Disk requirements: Whilst the space taken up for the application
    >>>> >>>> and
    >>> >>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>> >>> faster disks, including SSDs (solid state disks) and high speed hard
    >>> >>> disks, will speed up the response times of PostgreSQL or Oracle. For
    >>> >>> example, OpenClinica Optimized(tm) Hosting (Clinical Trials in the
    >>> >>> Cloud) uses Fusion-io's hybrid disk technology to improve database
    >>> >>> performance.
    >>> >>> Additionally, one user reported faster performance on the
    >>> >>> OpenClinica user list."
    >>>> >>>>
    >>>> >>>> If others are thinking about using SSDs, they should be aware that,
    >>>> >>>> just
    >>> >>> like regular hard drives, SSDs do fail
    >>> >>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,29
    >>> >>> 23.html) , and should be backed up regularly and use RAID where
    >>> >>> appropriate (as with regular hard drives).
    >>>> >>>>
    >>>> >>>> May and Cuneyt, were your versions of OpenClinica upgrades, or
    >>>> >>>> fresh
    >>> >>> installs? There was a fix for 404's and some consolidation of CSS
    >>> >>> that should have sped up 3.1.2 a little (mentioned on
    >>> >>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>> >>>>
    >>>> >>>> Yours,
    >>>> >>>>
    >>>> >>>> Michael
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>> >>> On Behalf Of Krister Kristianson
    >>>> >>>> Sent: 30 January 2012 13:40
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> A trick that I been very successful with is to put the database on
    >>>> >>>> a SSD
    >>> >>> drive. What took up to 10 seconds now takes less than 1 second using
    >>> >>> 3.1.2
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Xi, Xuemei
    >>>> >>>> Sent: 30 January 2012 14:29
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2
    >>>> >>>> is
    >>> >>> slower to load the page than OC3.1.1
    >>>> >>>>
    >>>> >>>> Thanks
    >>>> >>>> May
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Cuneyt Parlayan
    >>>> >>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> Hi all,
    >>>> >>>>
    >>>> >>>> We are having some performance problems in 3.1.2 which was not the
    >>>> >>>> case in
    >>> >>> earlier versions.
    >>>> >>>>
    >>>> >>>> When data is entered, it takes ± 5 seconds to open the window and
    >>> >>> another
    >>>> >>>> 5 seconds to save the data.
    >>>> >>>> This was not the case before.
    >>>> >>>> Anyone else experiencing this?
    >>>> >>>> Thanks, Cuneyt.
    >>>> >>>>
    >>>> >>>> --
    >>>> >>>> Cuneyt Parlayan
    >>>> >>>>
    >>>> >>>> Datamanager
    >>>> >>>> Department of Pathology
    >>>> >>>> VU University Medical Center
    >>>> >>>> Amsterdam - The Netherlands
    >>>> >>>>
  • kristiakkristiak Posts: 1,323 ✭✭✭
    Do you see this on a fresh install, not upgrade? Is it due to the use of
    many rules? As I said, I have divided my large CRF's into small sections
    that you save as you go along. This seems to avoid any performance issues.
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Cuneyt Parlayan
    Sent: 31 January 2012 10:29
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Michael,
    We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks for the
    information.
    I agree with Doug that this is a software issue. It looks like it is
    introduced in 3.1.2.
    I would also like to know what the OC project managers (Tom, Ben) think
    about this and what is their suggestion; that is, waiting for a software
    patch or upgrading the hardware to SSD's?
    Thanks, Cuneyt.
    On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    wrote:
    > > Hi Doug,
    > >
    > > Although I agree with you I do not have possibilities to do anything
    > > software wise!
    > >
    > > Regards
    > >
    > > Krister
    > >
    > > -----Original Message-----
    > >
    > > [mailto:[email protected]]
    > > On Behalf Of Douglas Bain
    > > Sent: 30 January 2012 17:54
    > > To: [email protected]
    > > Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    > >
    > > I would suggest looking more closely at the software than the hardware.
    > > Throwing fast hardware at the problem is a workaround, but not the
    solution.
    > > Typically an eCrf page submit or retrieval only effects a very small
    > > volume of data. A single subjects data may only be 5k. Waiting to read
    > > this off disks following disk index reads will always be slow in
    > > comparison to an in memory operation. Running sequential rules demands
    pre SQL optimisation.
    > >
    > > Doug Bain
    > >
    > >
    > > On 30 Jan 2012, at 16:28, "Michael Bluett" wrote:
    > >
    >> >> Dear Krister,
    >> >>
    >> >> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >> >> the
    > > Performance page in the OpenClinica Wikibook, thinking they would
    > > dramatically speed up OpenClinica, and your story provides further
    > > confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    > > disks that use SSDs):
    >> >>
    >> >> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >> >> "Disk requirements: Whilst the space taken up for the application and
    > > PostgreSQL are relatively small (Oracle's requirements will vary),
    > > faster disks, including SSDs (solid state disks) and high speed hard
    > > disks, will speed up the response times of PostgreSQL or Oracle. For
    > > example, OpenClinica Optimized(tm) Hosting (Clinical Trials in the
    > > Cloud) uses Fusion-io's hybrid disk technology to improve database
    performance.
    > > Additionally, one user reported faster performance on the OpenClinica
    > > user list."
    >> >>
    >> >> If others are thinking about using SSDs, they should be aware that,
    >> >> just
    > > like regular hard drives, SSDs do fail
    > > (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,2923
    > > .html) , and should be backed up regularly and use RAID where
    > > appropriate (as with regular hard drives).
    >> >>
    >> >> May and Cuneyt, were your versions of OpenClinica upgrades, or fresh
    > > installs? There was a fix for 404's and some consolidation of CSS
    > > that should have sped up 3.1.2 a little (mentioned on
    > > http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >> >>
    >> >> Yours,
    >> >>
    >> >> Michael
    >> >> -----Original Message-----
    >> >>
    >> >> [mailto:[email protected]]
    > > On Behalf Of Krister Kristianson
    >> >> Sent: 30 January 2012 13:40
    >> >> To: [email protected]
    >> >> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >> >>
    >> >> A trick that I been very successful with is to put the database on a
    >> >> SSD
    > > drive. What took up to 10 seconds now takes less than 1 second using
    > > 3.1.2
    >> >>
    >> >> Regards
    >> >>
    >> >> Krister
    >> >>
    >> >> -----Original Message-----
    >> >>
    >> >> [mailto:[email protected]]
    >> >> On Behalf Of Xi, Xuemei
    >> >> Sent: 30 January 2012 14:29
    >> >> To: [email protected]
    >> >> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >> >>
    >> >> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2 is
    > > slower to load the page than OC3.1.1
    >> >>
    >> >> Thanks
    >> >> May
    >> >>
    >> >> -----Original Message-----
    >> >>
    >> >> [mailto:[email protected]]
    >> >> On Behalf Of Cuneyt Parlayan
    >> >> Sent: Monday, January 30, 2012 3:30 AM
    >> >> To: [email protected]
    >> >> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >> >>
    >> >> Hi all,
    >> >>
    >> >> We are having some performance problems in 3.1.2 which was not the
    >> >> case in
    > > earlier versions.
    >> >>
    >> >> When data is entered, it takes ± 5 seconds to open the window and
    > > another
    >> >> 5 seconds to save the data.
    >> >> This was not the case before.
    >> >> Anyone else experiencing this?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> --
    >> >> Cuneyt Parlayan
    >> >>
    >> >> Datamanager
    >> >> Department of Pathology
    >> >> VU University Medical Center
    >> >> Amsterdam - The Netherlands
    >> >>
  • kristiakkristiak Posts: 1,323 ✭✭✭
    Strange, I do not see this at all in-spite-of some rather complex forms.
    What operating system do you use and how much RAM?
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 14:40
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I notice OC3.1.2 Performance issue relates to the rules and simple
    conditions. I am developing some CRF, no real data. When I load the initial
    CRF with 6 to 10 hilde/show conditions, it loads the page slow.
    When I save the testing data which will trigger the rules, it will save very
    slow and load the page.
    Best Regards,
    May
    -----Original Message-----
    On Behalf Of Cal Collins
    Sent: Tuesday, January 31, 2012 7:31 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben, Cuneyt,
    We are looking into what's happening. Any further detail you can provide on
    when this happens would be helpful (which URLs, the size of your database,
    your CRFs and rules, one user or multiple).
    Thanks,
    Cal
    -----Original Message-----
    On Behalf Of Cuneyt Parlayan
    Sent: Tuesday, January 31, 2012 7:43 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben,
    Thanks for your input.
    My postgres uses the defaults (I didn't change anything and followed the OC
    installation guide).
    During the upgrade I also followed the instructions provided by OC upgrade
    manual.
    Where are the "performance scripts"?
    How do you "REINDEX"?
    How do you change memory settings for postgress?
    Thanks,
    Cuneyt.
    PS: This is only happening in version 3.1.2. So it is not something that
    gradually happened, thats why I didn't suspect the database indexes.
    On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    > > Hello Cuneyt,
    > >
    > > Just to get the picture clearer:
    > > - did you run the performance scripts that created the extra indexes
    > > successfully?
    > > - how often do you do a REINDEX?
    > > - did you finetune your memorysettings for postgres?
    > >
    > > Kind regards,
    > >
    > > Gerben Rienk
    > >
    >> >> Hi Michael,
    >> >> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >> >> for the information.
    >> >> I agree with Doug that this is a software issue. It looks like it is
    >> >> introduced in 3.1.2.
    >> >> I would also like to know what the OC project managers (Tom, Ben)
    >> >> think about this and what is their suggestion; that is, waiting for a
    >> >> software patch or upgrading the hardware to SSD's?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >> >> wrote:
    >>> >>> Hi Doug,
    >>> >>>
    >>> >>> Although I agree with you I do not have possibilities to do anything
    >>> >>> software wise!
    >>> >>>
    >>> >>> Regards
    >>> >>>
    >>> >>> Krister
    >>> >>>
    >>> >>> -----Original Message-----
    >>> >>>
    >>> >>> [mailto:[email protected]]
    >>> >>> On Behalf Of Douglas Bain
    >>> >>> Sent: 30 January 2012 17:54
    >>> >>> To: [email protected]
    >>> >>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>> >>>
    >>> >>> I would suggest looking more closely at the software than the hardware.
    >>> >>> Throwing fast hardware at the problem is a workaround, but not the
    >>> >>> solution.
    >>> >>> Typically an eCrf page submit or retrieval only effects a very small
    >>> >>> volume of data. A single subjects data may only be 5k. Waiting to
    >>> >>> read this off disks following disk index reads will always be slow
    >>> >>> in comparison to an in memory operation. Running sequential rules
    >>> >>> demands pre SQL optimisation.
    >>> >>>
    >>> >>> Doug Bain
    >>> >>>
    >>> >>>
    >>> >>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>> >>> wrote:
    >>> >>>
    >>>> >>>> Dear Krister,
    >>>> >>>>
    >>>> >>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >>>> >>>> the
    >>> >>> Performance page in the OpenClinica Wikibook, thinking they would
    >>> >>> dramatically speed up OpenClinica, and your story provides further
    >>> >>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>> >>> disks that use SSDs):
    >>>> >>>>
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>> >>>> "Disk requirements: Whilst the space taken up for the application
    >>>> >>>> and
    >>> >>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>> >>> faster disks, including SSDs (solid state disks) and high speed hard
    >>> >>> disks, will speed up the response times of PostgreSQL or Oracle. For
    >>> >>> example, OpenClinica Optimized(tm) Hosting (Clinical Trials in the
    >>> >>> Cloud) uses Fusion-io's hybrid disk technology to improve database
    >>> >>> performance.
    >>> >>> Additionally, one user reported faster performance on the
    >>> >>> OpenClinica user list."
    >>>> >>>>
    >>>> >>>> If others are thinking about using SSDs, they should be aware that,
    >>>> >>>> just
    >>> >>> like regular hard drives, SSDs do fail
    >>> >>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,29
    >>> >>> 23.html) , and should be backed up regularly and use RAID where
    >>> >>> appropriate (as with regular hard drives).
    >>>> >>>>
    >>>> >>>> May and Cuneyt, were your versions of OpenClinica upgrades, or
    >>>> >>>> fresh
    >>> >>> installs? There was a fix for 404's and some consolidation of CSS
    >>> >>> that should have sped up 3.1.2 a little (mentioned on
    >>> >>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>> >>>>
    >>>> >>>> Yours,
    >>>> >>>>
    >>>> >>>> Michael
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>> >>> On Behalf Of Krister Kristianson
    >>>> >>>> Sent: 30 January 2012 13:40
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> A trick that I been very successful with is to put the database on
    >>>> >>>> a SSD
    >>> >>> drive. What took up to 10 seconds now takes less than 1 second using
    >>> >>> 3.1.2
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Xi, Xuemei
    >>>> >>>> Sent: 30 January 2012 14:29
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2
    >>>> >>>> is
    >>> >>> slower to load the page than OC3.1.1
    >>>> >>>>
    >>>> >>>> Thanks
    >>>> >>>> May
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Cuneyt Parlayan
    >>>> >>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> Hi all,
    >>>> >>>>
    >>>> >>>> We are having some performance problems in 3.1.2 which was not the
    >>>> >>>> case in
    >>> >>> earlier versions.
    >>>> >>>>
    >>>> >>>> When data is entered, it takes ± 5 seconds to open the window and
    >>> >>> another
    >>>> >>>> 5 seconds to save the data.
    >>>> >>>> This was not the case before.
    >>>> >>>> Anyone else experiencing this?
    >>>> >>>> Thanks, Cuneyt.
    >>>> >>>>
    >>>> >>>> --
    >>>> >>>> Cuneyt Parlayan
    >>>> >>>>
    >>>> >>>> Datamanager
    >>>> >>>> Department of Pathology
    >>>> >>>> VU University Medical Center
    >>>> >>>> Amsterdam - The Netherlands
    >>>> >>>>
  • GerbenRienkGerbenRienk Posts: 803 ✭✭✭
    Hi Cuneyt,
    The script to create about 150 indexes is in the Oracle part of the OC-zip
    (strangely enough, because the syntax is postgres and can not be applied
    to Oracle, unless you remove "USING btree").
    It may be that you have all these, but just to make sure.
    How to REINDEX is described on
    http://www.trialdatasolutions.com/tds/howto/postgresutils.jsp and with
    more technical detail on
    http://www.postgresql.org/docs/8.4/static/sql-reindex.html (In your
    situation with many users and many data you may want to shutdown the db
    and startup again with only access to postgres, because otherwise it may
    take too long.)
    The wikipage about tuning postgres is very good and to the point
    http://en.wikibooks.org/wiki/OpenClinica_User_Manual/OptimisingPostgreSQL
    I change the values a bit, depending on whether postgres is on a separate
    machine from tomcat or not and which other daemons are running.
    Experiment with the size for shared_buffers and adjust the rest
    accordingly, so effective_cache_size 2x shared_buffers,
    maintenance_work_mem 1/2 of shred_buffers, etc.
    Finally: I guess that in 3.1.2, more than in 3.1.1 the app relies more on
    indexes to retrieve the data.
    However if you do all the above and still get meager results you could
    also try to undeploy the app and deploy it again, or alternatively: stop
    tomcat, empty the work-directory and start tomcat again. I say this
    because sometimes when you have install a new version by replacing the
    war-file, this may cause problems. In general it is safer to undeploy the
    old version and only then deploy the new version.
    Hope this helps,
    Gerben Rienk Visser
    http://www.trialdatasolutions.com
    > > Hi Gerben,
    > >
    > > Thanks for your input.
    > >
    > > My postgres uses the defaults (I didn't change anything and followed
    > > the OC installation guide).
    > > During the upgrade I also followed the instructions provided by OC
    > > upgrade manual.
    > >
    > > Where are the "performance scripts"?
    > > How do you "REINDEX"?
    > > How do you change memory settings for postgress?
    > >
    > > Thanks,
    > > Cuneyt.
    > >
    > > PS: This is only happening in version 3.1.2. So it is not something
    > > that gradually happened, thats why I didn't suspect the database
    > > indexes.
    > >
    > > On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    >> >> Hello Cuneyt,
    >> >>
    >> >> Just to get the picture clearer:
    >> >> - did you run the performance scripts that created the extra indexes
    >> >> successfully?
    >> >> - how often do you do a REINDEX?
    >> >> - did you finetune your memorysettings for postgres?
    >> >>
    >> >> Kind regards,
    >> >>
    >> >> Gerben Rienk
    >> >>
    >>> >>> Hi Michael,
    >>> >>> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >>> >>> for the information.
    >>> >>> I agree with Doug that this is a software issue. It looks like it is
    >>> >>> introduced in 3.1.2.
    >>> >>> I would also like to know what the OC project managers (Tom, Ben)
    >>> >>> think about this and what is their suggestion; that is, waiting for a
    >>> >>> software patch or upgrading the hardware to SSD's?
    >>> >>> Thanks, Cuneyt.
    >>> >>>
    >>> >>> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >>> >>> wrote:
    >>>> >>>> Hi Doug,
    >>>> >>>>
    >>>> >>>> Although I agree with you I do not have possibilities to do anything
    >>>> >>>> software wise!
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Douglas Bain
    >>>> >>>> Sent: 30 January 2012 17:54
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> I would suggest looking more closely at the software than the
    >>>> >>>> hardware.
    >>>> >>>> Throwing fast hardware at the problem is a workaround, but not the
    >>>> >>>> solution.
    >>>> >>>> Typically an eCrf page submit or retrieval only effects a very small
    >>>> >>>> volume
    >>>> >>>> of data. A single subjects data may only be 5k. Waiting to read this
    >>>> >>>> off
    >>>> >>>> disks following disk index reads will always be slow in comparison to
    >>>> >>>> an
    >>>> >>>> in
    >>>> >>>> memory operation. Running sequential rules demands pre SQL
    >>>> >>>> optimisation.
    >>>> >>>>
    >>>> >>>> Doug Bain
    >>>> >>>>
    >>>> >>>>
    >>>> >>>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>>> >>>> wrote:
    >>>> >>>>
    >>>>> >>>>> Dear Krister,
    >>>>> >>>>>
    >>>>> >>>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >>>>> >>>>> the
    >>>> >>>> Performance page in the OpenClinica Wikibook, thinking they would
    >>>> >>>> dramatically speed up OpenClinica, and your story provides further
    >>>> >>>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>>> >>>> disks
    >>>> >>>> that use SSDs):
    >>>>> >>>>>
    >>>>> >>>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>>> >>>>> "Disk requirements: Whilst the space taken up for the application and
    >>>> >>>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>>> >>>> faster
    >>>> >>>> disks, including SSDs (solid state disks) and high speed hard disks,
    >>>> >>>> will
    >>>> >>>> speed up the response times of PostgreSQL or Oracle. For example,
    >>>> >>>> OpenClinica Optimized(tm) Hosting (Clinical Trials in the Cloud) uses
    >>>> >>>> Fusion-io's hybrid disk technology to improve database performance.
    >>>> >>>> Additionally, one user reported faster performance on the OpenClinica
    >>>> >>>> user
    >>>> >>>> list."
    >>>>> >>>>>
    >>>>> >>>>> If others are thinking about using SSDs, they should be aware that,
    >>>>> >>>>> just
    >>>> >>>> like regular hard drives, SSDs do fail
    >>>> >>>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,2923.html)
    >>>> >>>> , and should be backed up regularly and use RAID where appropriate (as
    >>>> >>>> with
    >>>> >>>> regular hard drives).
    >>>>> >>>>>
    >>>>> >>>>> May and Cuneyt, were your versions of OpenClinica upgrades, or fresh
    >>>> >>>> installs? There was a fix for 404's and some consolidation of CSS
    >>>> >>>> that
    >>>> >>>> should have sped up 3.1.2 a little (mentioned on
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>>> >>>>>
    >>>>> >>>>> Yours,
    >>>>> >>>>>
    >>>>> >>>>> Michael
    >>>>> >>>>> -----Original Message-----
    >>>>> >>>>>
    >>>>> >>>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Krister Kristianson
    >>>>> >>>>> Sent: 30 January 2012 13:40
    >>>>> >>>>> To: [email protected]
    >>>>> >>>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>>> >>>>>
    >>>>> >>>>> A trick that I been very successful with is to put the database on a
    >>>>> >>>>> SSD
    >>>> >>>> drive. What took up to 10 seconds now takes less than 1 second using
    >>>> >>>> 3.1.2
    >>>>> >>>>>
    >>>>> >>>>> Regards
    >>>>> >>>>>
    >>>>> >>>>> Krister
    >>>>> >>>>>
    >>>>> >>>>> -----Original Message-----
    >>>>> >>>>>
    >>>>> >>>>> [mailto:[email protected]]
    >>>>> >>>>> On Behalf Of Xi, Xuemei
    >>>>> >>>>> Sent: 30 January 2012 14:29
    >>>>> >>>>> To: [email protected]
    >>>>> >>>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>>> >>>>>
    >>>>> >>>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2 is
    >>>> >>>> slower to load the page than OC3.1.1
    >>>>> >>>>>
    >>>>> >>>>> Thanks
    >>>>> >>>>> May
    >>>>> >>>>>
    >>>>> >>>>> -----Original Message-----
    >>>>> >>>>>
    >>>>> >>>>> [mailto:[email protected]]
    >>>>> >>>>> On Behalf Of Cuneyt Parlayan
    >>>>> >>>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>>> >>>>> To: [email protected]
    >>>>> >>>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>>> >>>>>
    >>>>> >>>>> Hi all,
    >>>>> >>>>>
    >>>>> >>>>> We are having some performance problems in 3.1.2 which was not the
    >>>>> >>>>> case
    >>>>> >>>>> in
    >>>> >>>> earlier versions.
    >>>>> >>>>>
    >>>>> >>>>> When data is entered, it takes ± 5 seconds to open the window and
    >>>> >>>> another
    >>>>> >>>>> 5 seconds to save the data.
    >>>>> >>>>> This was not the case before.
    >>>>> >>>>> Anyone else experiencing this?
    >>>>> >>>>> Thanks, Cuneyt.
    >>>>> >>>>>
    >>>>> >>>>> --
    >>>>> >>>>> Cuneyt Parlayan
    >>>>> >>>>>
    >>>>> >>>>> Datamanager
    >>>>> >>>>> Department of Pathology
    >>>>> >>>>> VU University Medical Center
    >>>>> >>>>> Amsterdam - The Netherlands
    >>>>> >>>>>
  • mx8866mx8866 Posts: 109
    I have fresh install OC3.1.2, not upgrade. Server is HP DL320 with 2G memory. I only have 20 records testing data. They are SIMPLE 2 or 3 rules for show/hide condition. I notice it is very slow to save the data with these Rules in the CRFs.
    Regards
    May
    -----Original Message-----
    Sent: Tuesday, January 31, 2012 7:49 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Strange, I do not see this at all in-spite-of some rather complex forms.
    What operating system do you use and how much RAM?
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 14:40
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I notice OC3.1.2 Performance issue relates to the rules and simple conditions. I am developing some CRF, no real data. When I load the initial CRF with 6 to 10 hilde/show conditions, it loads the page slow.
    When I save the testing data which will trigger the rules, it will save very slow and load the page.
    Best Regards,
    May
    -----Original Message-----
    On Behalf Of Cal Collins
    Sent: Tuesday, January 31, 2012 7:31 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben, Cuneyt,
    We are looking into what's happening. Any further detail you can provide on when this happens would be helpful (which URLs, the size of your database, your CRFs and rules, one user or multiple).
    Thanks,
    Cal
    -----Original Message-----
    On Behalf Of Cuneyt Parlayan
    Sent: Tuesday, January 31, 2012 7:43 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben,
    Thanks for your input.
    My postgres uses the defaults (I didn't change anything and followed the OC installation guide).
    During the upgrade I also followed the instructions provided by OC upgrade manual.
    Where are the "performance scripts"?
    How do you "REINDEX"?
    How do you change memory settings for postgress?
    Thanks,
    Cuneyt.
    PS: This is only happening in version 3.1.2. So it is not something that gradually happened, thats why I didn't suspect the database indexes.
    On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    > > Hello Cuneyt,
    > >
    > > Just to get the picture clearer:
    > > - did you run the performance scripts that created the extra indexes
    > > successfully?
    > > - how often do you do a REINDEX?
    > > - did you finetune your memorysettings for postgres?
    > >
    > > Kind regards,
    > >
    > > Gerben Rienk
    > >
    >> >> Hi Michael,
    >> >> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >> >> for the information.
    >> >> I agree with Doug that this is a software issue. It looks like it is
    >> >> introduced in 3.1.2.
    >> >> I would also like to know what the OC project managers (Tom, Ben)
    >> >> think about this and what is their suggestion; that is, waiting for a
    >> >> software patch or upgrading the hardware to SSD's?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >> >> wrote:
    >>> >>> Hi Doug,
    >>> >>>
    >>> >>> Although I agree with you I do not have possibilities to do anything
    >>> >>> software wise!
    >>> >>>
    >>> >>> Regards
    >>> >>>
    >>> >>> Krister
    >>> >>>
    >>> >>> -----Original Message-----
    >>> >>>
    >>> >>> [mailto:[email protected]]
    >>> >>> On Behalf Of Douglas Bain
    >>> >>> Sent: 30 January 2012 17:54
    >>> >>> To: [email protected]
    >>> >>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>> >>>
    >>> >>> I would suggest looking more closely at the software than the hardware.
    >>> >>> Throwing fast hardware at the problem is a workaround, but not the
    >>> >>> solution.
    >>> >>> Typically an eCrf page submit or retrieval only effects a very small
    >>> >>> volume of data. A single subjects data may only be 5k. Waiting to
    >>> >>> read this off disks following disk index reads will always be slow
    >>> >>> in comparison to an in memory operation. Running sequential rules
    >>> >>> demands pre SQL optimisation.
    >>> >>>
    >>> >>> Doug Bain
    >>> >>>
    >>> >>>
    >>> >>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>> >>> wrote:
    >>> >>>
    >>>> >>>> Dear Krister,
    >>>> >>>>
    >>>> >>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >>>> >>>> the
    >>> >>> Performance page in the OpenClinica Wikibook, thinking they would
    >>> >>> dramatically speed up OpenClinica, and your story provides further
    >>> >>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>> >>> disks that use SSDs):
    >>>> >>>>
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>> >>>> "Disk requirements: Whilst the space taken up for the application
    >>>> >>>> and
    >>> >>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>> >>> faster disks, including SSDs (solid state disks) and high speed hard
    >>> >>> disks, will speed up the response times of PostgreSQL or Oracle. For
    >>> >>> example, OpenClinica Optimized(tm) Hosting (Clinical Trials in the
    >>> >>> Cloud) uses Fusion-io's hybrid disk technology to improve database
    >>> >>> performance.
    >>> >>> Additionally, one user reported faster performance on the
    >>> >>> OpenClinica user list."
    >>>> >>>>
    >>>> >>>> If others are thinking about using SSDs, they should be aware that,
    >>>> >>>> just
    >>> >>> like regular hard drives, SSDs do fail
    >>> >>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,29
    >>> >>> 23.html) , and should be backed up regularly and use RAID where
    >>> >>> appropriate (as with regular hard drives).
    >>>> >>>>
    >>>> >>>> May and Cuneyt, were your versions of OpenClinica upgrades, or
    >>>> >>>> fresh
    >>> >>> installs? There was a fix for 404's and some consolidation of CSS
    >>> >>> that should have sped up 3.1.2 a little (mentioned on
    >>> >>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>> >>>>
    >>>> >>>> Yours,
    >>>> >>>>
    >>>> >>>> Michael
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>> >>> On Behalf Of Krister Kristianson
    >>>> >>>> Sent: 30 January 2012 13:40
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> A trick that I been very successful with is to put the database on
    >>>> >>>> a SSD
    >>> >>> drive. What took up to 10 seconds now takes less than 1 second using
    >>> >>> 3.1.2
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Xi, Xuemei
    >>>> >>>> Sent: 30 January 2012 14:29
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2
    >>>> >>>> is
    >>> >>> slower to load the page than OC3.1.1
    >>>> >>>>
    >>>> >>>> Thanks
    >>>> >>>> May
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Cuneyt Parlayan
    >>>> >>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> Hi all,
    >>>> >>>>
    >>>> >>>> We are having some performance problems in 3.1.2 which was not the
    >>>> >>>> case in
    >>> >>> earlier versions.
    >>>> >>>>
    >>>> >>>> When data is entered, it takes ± 5 seconds to open the window and
    >>> >>> another
    >>>> >>>> 5 seconds to save the data.
    >>>> >>>> This was not the case before.
    >>>> >>>> Anyone else experiencing this?
    >>>> >>>> Thanks, Cuneyt.
    >>>> >>>>
    >>>> >>>> --
    >>>> >>>> Cuneyt Parlayan
    >>>> >>>>
    >>>> >>>> Datamanager
    >>>> >>>> Department of Pathology
    >>>> >>>> VU University Medical Center
    >>>> >>>> Amsterdam - The Netherlands
    >>>> >>>>
  • ccollinsccollins Posts: 378 admin
    Hi May,
    Can you define 'very slow'? Also, if you can share your CRFs and rules
    that would be very helpful.
    Thanks, Cal
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Xi, Xuemei
    Sent: Tuesday, January 31, 2012 9:02 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I have fresh install OC3.1.2, not upgrade. Server is HP DL320 with 2G
    memory. I only have 20 records testing data. They are SIMPLE 2 or 3
    rules for show/hide condition. I notice it is very slow to save the data
    with these Rules in the CRFs.
    Regards
    May
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Krister Kristianson
    Sent: Tuesday, January 31, 2012 7:49 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Strange, I do not see this at all in-spite-of some rather complex forms.
    What operating system do you use and how much RAM?
    Regards
    Krister
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 14:40
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I notice OC3.1.2 Performance issue relates to the rules and simple
    conditions. I am developing some CRF, no real data. When I load the
    initial CRF with 6 to 10 hilde/show conditions, it loads the page slow.
    When I save the testing data which will trigger the rules, it will save
    very slow and load the page.
    Best Regards,
    May
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Cal Collins
    Sent: Tuesday, January 31, 2012 7:31 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben, Cuneyt,
    We are looking into what's happening. Any further detail you can provide
    on when this happens would be helpful (which URLs, the size of your
    database, your CRFs and rules, one user or multiple).
    Thanks,
    Cal
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Cuneyt Parlayan
    Sent: Tuesday, January 31, 2012 7:43 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben,
    Thanks for your input.
    My postgres uses the defaults (I didn't change anything and followed the
    OC installation guide).
    During the upgrade I also followed the instructions provided by OC
    upgrade manual.
    Where are the "performance scripts"?
    How do you "REINDEX"?
    How do you change memory settings for postgress?
    Thanks,
    Cuneyt.
    PS: This is only happening in version 3.1.2. So it is not something that
    gradually happened, thats why I didn't suspect the database indexes.
    On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    > > Hello Cuneyt,
    > >
    > > Just to get the picture clearer:
    > > - did you run the performance scripts that created the extra indexes
    > > successfully?
    > > - how often do you do a REINDEX?
    > > - did you finetune your memorysettings for postgres?
    > >
    > > Kind regards,
    > >
    > > Gerben Rienk
    > >
    >> >> Hi Michael,
    >> >> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >> >> for the information.
    >> >> I agree with Doug that this is a software issue. It looks like it is
    >> >> introduced in 3.1.2.
    >> >> I would also like to know what the OC project managers (Tom, Ben)
    >> >> think about this and what is their suggestion; that is, waiting for a
    >> >> software patch or upgrading the hardware to SSD's?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >> >> wrote:
    >>> >>> Hi Doug,
    >>> >>>
    >>> >>> Although I agree with you I do not have possibilities to do anything
    >>> >>> software wise!
    >>> >>>
    >>> >>> Regards
    >>> >>>
    >>> >>> Krister
    >>> >>>
    >>> >>> -----Original Message-----
    >>> >>>
    >>> >>> [mailto:[email protected]]
    >>> >>> On Behalf Of Douglas Bain
    >>> >>> Sent: 30 January 2012 17:54
    >>> >>> To: [email protected]
    >>> >>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>> >>>
    >>> >>> I would suggest looking more closely at the software than the
    hardware.
    >>> >>> Throwing fast hardware at the problem is a workaround, but not the
    >>> >>> solution.
    >>> >>> Typically an eCrf page submit or retrieval only effects a very small
    >>> >>> volume of data. A single subjects data may only be 5k. Waiting to
    >>> >>> read this off disks following disk index reads will always be slow
    >>> >>> in comparison to an in memory operation. Running sequential rules
    >>> >>> demands pre SQL optimisation.
    >>> >>>
    >>> >>> Doug Bain
    >>> >>>
    >>> >>>
    >>> >>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>> >>> wrote:
    >>> >>>
    >>>> >>>> Dear Krister,
    >>>> >>>>
    >>>> >>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >>>> >>>> the
    >>> >>> Performance page in the OpenClinica Wikibook, thinking they would
    >>> >>> dramatically speed up OpenClinica, and your story provides further
    >>> >>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>> >>> disks that use SSDs):
    >>>> >>>>
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>> >>>> "Disk requirements: Whilst the space taken up for the application
    >>>> >>>> and
    >>> >>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>> >>> faster disks, including SSDs (solid state disks) and high speed hard
    >>> >>> disks, will speed up the response times of PostgreSQL or Oracle. For
    >>> >>> example, OpenClinica Optimized(tm) Hosting (Clinical Trials in the
    >>> >>> Cloud) uses Fusion-io's hybrid disk technology to improve database
    >>> >>> performance.
    >>> >>> Additionally, one user reported faster performance on the
    >>> >>> OpenClinica user list."
    >>>> >>>>
    >>>> >>>> If others are thinking about using SSDs, they should be aware that,
    >>>> >>>> just
    >>> >>> like regular hard drives, SSDs do fail
    >>> >>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,29
    >>> >>> 23.html) , and should be backed up regularly and use RAID where
    >>> >>> appropriate (as with regular hard drives).
    >>>> >>>>
    >>>> >>>> May and Cuneyt, were your versions of OpenClinica upgrades, or
    >>>> >>>> fresh
    >>> >>> installs? There was a fix for 404's and some consolidation of CSS
    >>> >>> that should have sped up 3.1.2 a little (mentioned on
    >>> >>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>> >>>>
    >>>> >>>> Yours,
    >>>> >>>>
    >>>> >>>> Michael
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>> >>> On Behalf Of Krister Kristianson
    >>>> >>>> Sent: 30 January 2012 13:40
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> A trick that I been very successful with is to put the database on
    >>>> >>>> a SSD
    >>> >>> drive. What took up to 10 seconds now takes less than 1 second using
    >>> >>> 3.1.2
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Xi, Xuemei
    >>>> >>>> Sent: 30 January 2012 14:29
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2
    >>>> >>>> is
    >>> >>> slower to load the page than OC3.1.1
    >>>> >>>>
    >>>> >>>> Thanks
    >>>> >>>> May
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Cuneyt Parlayan
    >>>> >>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> Hi all,
    >>>> >>>>
    >>>> >>>> We are having some performance problems in 3.1.2 which was not the
    >>>> >>>> case in
    >>> >>> earlier versions.
    >>>> >>>>
    >>>> >>>> When data is entered, it takes ± 5 seconds to open the window and
    >>> >>> another
    >>>> >>>> 5 seconds to save the data.
    >>>> >>>> This was not the case before.
    >>>> >>>> Anyone else experiencing this?
    >>>> >>>> Thanks, Cuneyt.
    >>>> >>>>
    >>>> >>>> --
    >>>> >>>> Cuneyt Parlayan
    >>>> >>>>
    >>>> >>>> Datamanager
    >>>> >>>> Department of Pathology
    >>>> >>>> VU University Medical Center
    >>>> >>>> Amsterdam - The Netherlands
    >>>> >>>>
  • mx8866mx8866 Posts: 109
    Does 10 seconds loading the page is slow? I restart the server. It seems help. I can share my CRFs if the experts think it is slow.
    Best Regards
    May
    -----Original Message-----
    Sent: Tuesday, January 31, 2012 8:08 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi May,
    Can you define 'very slow'? Also, if you can share your CRFs and rules that would be very helpful.
    Thanks, Cal
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Xi, Xuemei
    Sent: Tuesday, January 31, 2012 9:02 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I have fresh install OC3.1.2, not upgrade. Server is HP DL320 with 2G memory. I only have 20 records testing data. They are SIMPLE 2 or 3 rules for show/hide condition. I notice it is very slow to save the data with these Rules in the CRFs.
    Regards
    May
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Krister Kristianson
    Sent: Tuesday, January 31, 2012 7:49 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Strange, I do not see this at all in-spite-of some rather complex forms.
    What operating system do you use and how much RAM?
    Regards
    Krister
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 14:40
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I notice OC3.1.2 Performance issue relates to the rules and simple conditions. I am developing some CRF, no real data. When I load the initial CRF with 6 to 10 hilde/show conditions, it loads the page slow.
    When I save the testing data which will trigger the rules, it will save very slow and load the page.
    Best Regards,
    May
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Cal Collins
    Sent: Tuesday, January 31, 2012 7:31 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben, Cuneyt,
    We are looking into what's happening. Any further detail you can provide on when this happens would be helpful (which URLs, the size of your database, your CRFs and rules, one user or multiple).
    Thanks,
    Cal
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Cuneyt Parlayan
    Sent: Tuesday, January 31, 2012 7:43 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben,
    Thanks for your input.
    My postgres uses the defaults (I didn't change anything and followed the OC installation guide).
    During the upgrade I also followed the instructions provided by OC upgrade manual.
    Where are the "performance scripts"?
    How do you "REINDEX"?
    How do you change memory settings for postgress?
    Thanks,
    Cuneyt.
    PS: This is only happening in version 3.1.2. So it is not something that gradually happened, thats why I didn't suspect the database indexes.
    On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    > > Hello Cuneyt,
    > >
    > > Just to get the picture clearer:
    > > - did you run the performance scripts that created the extra indexes
    > > successfully?
    > > - how often do you do a REINDEX?
    > > - did you finetune your memorysettings for postgres?
    > >
    > > Kind regards,
    > >
    > > Gerben Rienk
    > >
    >> >> Hi Michael,
    >> >> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >> >> for the information.
    >> >> I agree with Doug that this is a software issue. It looks like it is
    >> >> introduced in 3.1.2.
    >> >> I would also like to know what the OC project managers (Tom, Ben)
    >> >> think about this and what is their suggestion; that is, waiting for a
    >> >> software patch or upgrading the hardware to SSD's?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >> >> wrote:
    >>> >>> Hi Doug,
    >>> >>>
    >>> >>> Although I agree with you I do not have possibilities to do anything
    >>> >>> software wise!
    >>> >>>
    >>> >>> Regards
    >>> >>>
    >>> >>> Krister
    >>> >>>
    >>> >>> -----Original Message-----
    >>> >>>
    >>> >>> [mailto:[email protected]]
    >>> >>> On Behalf Of Douglas Bain
    >>> >>> Sent: 30 January 2012 17:54
    >>> >>> To: [email protected]
    >>> >>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>> >>>
    >>> >>> I would suggest looking more closely at the software than the
    hardware.
    >>> >>> Throwing fast hardware at the problem is a workaround, but not the
    >>> >>> solution.
    >>> >>> Typically an eCrf page submit or retrieval only effects a very small
    >>> >>> volume of data. A single subjects data may only be 5k. Waiting to
    >>> >>> read this off disks following disk index reads will always be slow
    >>> >>> in comparison to an in memory operation. Running sequential rules
    >>> >>> demands pre SQL optimisation.
    >>> >>>
    >>> >>> Doug Bain
    >>> >>>
    >>> >>>
    >>> >>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>> >>> wrote:
    >>> >>>
    >>>> >>>> Dear Krister,
    >>>> >>>>
    >>>> >>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >>>> >>>> the
    >>> >>> Performance page in the OpenClinica Wikibook, thinking they would
    >>> >>> dramatically speed up OpenClinica, and your story provides further
    >>> >>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>> >>> disks that use SSDs):
    >>>> >>>>
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>> >>>> "Disk requirements: Whilst the space taken up for the application
    >>>> >>>> and
    >>> >>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>> >>> faster disks, including SSDs (solid state disks) and high speed hard
    >>> >>> disks, will speed up the response times of PostgreSQL or Oracle. For
    >>> >>> example, OpenClinica Optimized(tm) Hosting (Clinical Trials in the
    >>> >>> Cloud) uses Fusion-io's hybrid disk technology to improve database
    >>> >>> performance.
    >>> >>> Additionally, one user reported faster performance on the
    >>> >>> OpenClinica user list."
    >>>> >>>>
    >>>> >>>> If others are thinking about using SSDs, they should be aware that,
    >>>> >>>> just
    >>> >>> like regular hard drives, SSDs do fail
    >>> >>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,29
    >>> >>> 23.html) , and should be backed up regularly and use RAID where
    >>> >>> appropriate (as with regular hard drives).
    >>>> >>>>
    >>>> >>>> May and Cuneyt, were your versions of OpenClinica upgrades, or
    >>>> >>>> fresh
    >>> >>> installs? There was a fix for 404's and some consolidation of CSS
    >>> >>> that should have sped up 3.1.2 a little (mentioned on
    >>> >>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>> >>>>
    >>>> >>>> Yours,
    >>>> >>>>
    >>>> >>>> Michael
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>> >>> On Behalf Of Krister Kristianson
    >>>> >>>> Sent: 30 January 2012 13:40
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> A trick that I been very successful with is to put the database on
    >>>> >>>> a SSD
    >>> >>> drive. What took up to 10 seconds now takes less than 1 second using
    >>> >>> 3.1.2
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Xi, Xuemei
    >>>> >>>> Sent: 30 January 2012 14:29
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2
    >>>> >>>> is
    >>> >>> slower to load the page than OC3.1.1
    >>>> >>>>
    >>>> >>>> Thanks
    >>>> >>>> May
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Cuneyt Parlayan
    >>>> >>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> Hi all,
    >>>> >>>>
    >>>> >>>> We are having some performance problems in 3.1.2 which was not the
    >>>> >>>> case in
    >>> >>> earlier versions.
    >>>> >>>>
    >>>> >>>> When data is entered, it takes ± 5 seconds to open the window and
    >>> >>> another
    >>>> >>>> 5 seconds to save the data.
    >>>> >>>> This was not the case before.
    >>>> >>>> Anyone else experiencing this?
    >>>> >>>> Thanks, Cuneyt.
    >>>> >>>>
    >>>> >>>> --
    >>>> >>>> Cuneyt Parlayan
    >>>> >>>>
    >>>> >>>> Datamanager
    >>>> >>>> Department of Pathology
    >>>> >>>> VU University Medical Center
    >>>> >>>> Amsterdam - The Netherlands
    >>>> >>>>
  • ccollinsccollins Posts: 378 admin
    That's pretty slow for a small simple CRF. Yes, please share and we'll
    try to replicate your observations here.
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Xi, Xuemei
    Sent: Tuesday, January 31, 2012 9:21 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Does 10 seconds loading the page is slow? I restart the server. It seems
    help. I can share my CRFs if the experts think it is slow.
    Best Regards
    May
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Cal Collins
    Sent: Tuesday, January 31, 2012 8:08 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi May,
    Can you define 'very slow'? Also, if you can share your CRFs and rules
    that would be very helpful.
    Thanks, Cal
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Xi, Xuemei
    Sent: Tuesday, January 31, 2012 9:02 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I have fresh install OC3.1.2, not upgrade. Server is HP DL320 with 2G
    memory. I only have 20 records testing data. They are SIMPLE 2 or 3
    rules for show/hide condition. I notice it is very slow to save the data
    with these Rules in the CRFs.
    Regards
    May
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Krister Kristianson
    Sent: Tuesday, January 31, 2012 7:49 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Strange, I do not see this at all in-spite-of some rather complex forms.
    What operating system do you use and how much RAM?
    Regards
    Krister
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 14:40
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I notice OC3.1.2 Performance issue relates to the rules and simple
    conditions. I am developing some CRF, no real data. When I load the
    initial CRF with 6 to 10 hilde/show conditions, it loads the page slow.
    When I save the testing data which will trigger the rules, it will save
    very slow and load the page.
    Best Regards,
    May
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Cal Collins
    Sent: Tuesday, January 31, 2012 7:31 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben, Cuneyt,
    We are looking into what's happening. Any further detail you can provide
    on when this happens would be helpful (which URLs, the size of your
    database, your CRFs and rules, one user or multiple).
    Thanks,
    Cal
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Cuneyt Parlayan
    Sent: Tuesday, January 31, 2012 7:43 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben,
    Thanks for your input.
    My postgres uses the defaults (I didn't change anything and followed the
    OC installation guide).
    During the upgrade I also followed the instructions provided by OC
    upgrade manual.
    Where are the "performance scripts"?
    How do you "REINDEX"?
    How do you change memory settings for postgress?
    Thanks,
    Cuneyt.
    PS: This is only happening in version 3.1.2. So it is not something that
    gradually happened, thats why I didn't suspect the database indexes.
    On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    > > Hello Cuneyt,
    > >
    > > Just to get the picture clearer:
    > > - did you run the performance scripts that created the extra indexes
    > > successfully?
    > > - how often do you do a REINDEX?
    > > - did you finetune your memorysettings for postgres?
    > >
    > > Kind regards,
    > >
    > > Gerben Rienk
    > >
    >> >> Hi Michael,
    >> >> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >> >> for the information.
    >> >> I agree with Doug that this is a software issue. It looks like it is
    >> >> introduced in 3.1.2.
    >> >> I would also like to know what the OC project managers (Tom, Ben)
    >> >> think about this and what is their suggestion; that is, waiting for a
    >> >> software patch or upgrading the hardware to SSD's?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >> >> wrote:
    >>> >>> Hi Doug,
    >>> >>>
    >>> >>> Although I agree with you I do not have possibilities to do anything
    >>> >>> software wise!
    >>> >>>
    >>> >>> Regards
    >>> >>>
    >>> >>> Krister
    >>> >>>
    >>> >>> -----Original Message-----
    >>> >>>
    >>> >>> [mailto:[email protected]]
    >>> >>> On Behalf Of Douglas Bain
    >>> >>> Sent: 30 January 2012 17:54
    >>> >>> To: [email protected]
    >>> >>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>> >>>
    >>> >>> I would suggest looking more closely at the software than the
    hardware.
    >>> >>> Throwing fast hardware at the problem is a workaround, but not the
    >>> >>> solution.
    >>> >>> Typically an eCrf page submit or retrieval only effects a very small
    >>> >>> volume of data. A single subjects data may only be 5k. Waiting to
    >>> >>> read this off disks following disk index reads will always be slow
    >>> >>> in comparison to an in memory operation. Running sequential rules
    >>> >>> demands pre SQL optimisation.
    >>> >>>
    >>> >>> Doug Bain
    >>> >>>
    >>> >>>
    >>> >>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>> >>> wrote:
    >>> >>>
    >>>> >>>> Dear Krister,
    >>>> >>>>
    >>>> >>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >>>> >>>> the
    >>> >>> Performance page in the OpenClinica Wikibook, thinking they would
    >>> >>> dramatically speed up OpenClinica, and your story provides further
    >>> >>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>> >>> disks that use SSDs):
    >>>> >>>>
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>> >>>> "Disk requirements: Whilst the space taken up for the application
    >>>> >>>> and
    >>> >>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>> >>> faster disks, including SSDs (solid state disks) and high speed hard
    >>> >>> disks, will speed up the response times of PostgreSQL or Oracle. For
    >>> >>> example, OpenClinica Optimized(tm) Hosting (Clinical Trials in the
    >>> >>> Cloud) uses Fusion-io's hybrid disk technology to improve database
    >>> >>> performance.
    >>> >>> Additionally, one user reported faster performance on the
    >>> >>> OpenClinica user list."
    >>>> >>>>
    >>>> >>>> If others are thinking about using SSDs, they should be aware that,
    >>>> >>>> just
    >>> >>> like regular hard drives, SSDs do fail
    >>> >>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,29
    >>> >>> 23.html) , and should be backed up regularly and use RAID where
    >>> >>> appropriate (as with regular hard drives).
    >>>> >>>>
    >>>> >>>> May and Cuneyt, were your versions of OpenClinica upgrades, or
    >>>> >>>> fresh
    >>> >>> installs? There was a fix for 404's and some consolidation of CSS
    >>> >>> that should have sped up 3.1.2 a little (mentioned on
    >>> >>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>> >>>>
    >>>> >>>> Yours,
    >>>> >>>>
    >>>> >>>> Michael
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>> >>> On Behalf Of Krister Kristianson
    >>>> >>>> Sent: 30 January 2012 13:40
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> A trick that I been very successful with is to put the database on
    >>>> >>>> a SSD
    >>> >>> drive. What took up to 10 seconds now takes less than 1 second using
    >>> >>> 3.1.2
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Xi, Xuemei
    >>>> >>>> Sent: 30 January 2012 14:29
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2
    >>>> >>>> is
    >>> >>> slower to load the page than OC3.1.1
    >>>> >>>>
    >>>> >>>> Thanks
    >>>> >>>> May
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Cuneyt Parlayan
    >>>> >>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> Hi all,
    >>>> >>>>
    >>>> >>>> We are having some performance problems in 3.1.2 which was not the
    >>>> >>>> case in
    >>> >>> earlier versions.
    >>>> >>>>
    >>>> >>>> When data is entered, it takes ± 5 seconds to open the window and
    >>> >>> another
    >>>> >>>> 5 seconds to save the data.
    >>>> >>>> This was not the case before.
    >>>> >>>> Anyone else experiencing this?
    >>>> >>>> Thanks, Cuneyt.
    >>>> >>>>
    >>>> >>>> --
    >>>> >>>> Cuneyt Parlayan
    >>>> >>>>
    >>>> >>>> Datamanager
    >>>> >>>> Department of Pathology
    >>>> >>>> VU University Medical Center
    >>>> >>>> Amsterdam - The Netherlands
    >>>> >>>>
  • mx8866mx8866 Posts: 109
    Here are my CRF with 3 rules. Maybe the experts can think a way to redesign this.
    The rules: When you select the other locations or the other Blood Products or the other Fluids, it should load the other group of repeat values to let the users to specify the other "location", "blood product" or "IV fluids".
    Regards
    May
    -----Original Message-----
    Sent: Tuesday, January 31, 2012 8:26 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    That's pretty slow for a small simple CRF. Yes, please share and we'll try to replicate your observations here.
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Xi, Xuemei
    Sent: Tuesday, January 31, 2012 9:21 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Does 10 seconds loading the page is slow? I restart the server. It seems help. I can share my CRFs if the experts think it is slow.
    Best Regards
    May
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Cal Collins
    Sent: Tuesday, January 31, 2012 8:08 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi May,
    Can you define 'very slow'? Also, if you can share your CRFs and rules that would be very helpful.
    Thanks, Cal
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Xi, Xuemei
    Sent: Tuesday, January 31, 2012 9:02 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I have fresh install OC3.1.2, not upgrade. Server is HP DL320 with 2G memory. I only have 20 records testing data. They are SIMPLE 2 or 3 rules for show/hide condition. I notice it is very slow to save the data with these Rules in the CRFs.
    Regards
    May
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Krister Kristianson
    Sent: Tuesday, January 31, 2012 7:49 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Strange, I do not see this at all in-spite-of some rather complex forms.
    What operating system do you use and how much RAM?
    Regards
    Krister
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 14:40
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    I notice OC3.1.2 Performance issue relates to the rules and simple conditions. I am developing some CRF, no real data. When I load the initial CRF with 6 to 10 hilde/show conditions, it loads the page slow.
    When I save the testing data which will trigger the rules, it will save very slow and load the page.
    Best Regards,
    May
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Cal Collins
    Sent: Tuesday, January 31, 2012 7:31 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben, Cuneyt,
    We are looking into what's happening. Any further detail you can provide on when this happens would be helpful (which URLs, the size of your database, your CRFs and rules, one user or multiple).
    Thanks,
    Cal
    -----Original Message-----
    [mailto:[email protected]]
    On Behalf Of Cuneyt Parlayan
    Sent: Tuesday, January 31, 2012 7:43 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Gerben,
    Thanks for your input.
    My postgres uses the defaults (I didn't change anything and followed the OC installation guide).
    During the upgrade I also followed the instructions provided by OC upgrade manual.
    Where are the "performance scripts"?
    How do you "REINDEX"?
    How do you change memory settings for postgress?
    Thanks,
    Cuneyt.
    PS: This is only happening in version 3.1.2. So it is not something that gradually happened, thats why I didn't suspect the database indexes.
    On Tue, Jan 31, 2012 at 11:57 AM, Gerben Rienk wrote:
    > > Hello Cuneyt,
    > >
    > > Just to get the picture clearer:
    > > - did you run the performance scripts that created the extra indexes
    > > successfully?
    > > - how often do you do a REINDEX?
    > > - did you finetune your memorysettings for postgres?
    > >
    > > Kind regards,
    > >
    > > Gerben Rienk
    > >
    >> >> Hi Michael,
    >> >> We have upgraded from 3.1 to 3.1.2 conform OC upgrade manual. Thanks
    >> >> for the information.
    >> >> I agree with Doug that this is a software issue. It looks like it is
    >> >> introduced in 3.1.2.
    >> >> I would also like to know what the OC project managers (Tom, Ben)
    >> >> think about this and what is their suggestion; that is, waiting for a
    >> >> software patch or upgrading the hardware to SSD's?
    >> >> Thanks, Cuneyt.
    >> >>
    >> >> On Mon, Jan 30, 2012 at 6:13 PM, Krister Kristianson
    >> >> wrote:
    >>> >>> Hi Doug,
    >>> >>>
    >>> >>> Although I agree with you I do not have possibilities to do anything
    >>> >>> software wise!
    >>> >>>
    >>> >>> Regards
    >>> >>>
    >>> >>> Krister
    >>> >>>
    >>> >>> -----Original Message-----
    >>> >>>
    >>> >>> [mailto:[email protected]]
    >>> >>> On Behalf Of Douglas Bain
    >>> >>> Sent: 30 January 2012 17:54
    >>> >>> To: [email protected]
    >>> >>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>> >>>
    >>> >>> I would suggest looking more closely at the software than the
    hardware.
    >>> >>> Throwing fast hardware at the problem is a workaround, but not the
    >>> >>> solution.
    >>> >>> Typically an eCrf page submit or retrieval only effects a very small
    >>> >>> volume of data. A single subjects data may only be 5k. Waiting to
    >>> >>> read this off disks following disk index reads will always be slow
    >>> >>> in comparison to an in memory operation. Running sequential rules
    >>> >>> demands pre SQL optimisation.
    >>> >>>
    >>> >>> Doug Bain
    >>> >>>
    >>> >>>
    >>> >>> On 30 Jan 2012, at 16:28, "Michael Bluett"
    >>> >>> wrote:
    >>> >>>
    >>>> >>>> Dear Krister,
    >>>> >>>>
    >>>> >>>> Thanks for mentioning that, I mentioned SSDs (solid state disks) on
    >>>> >>>> the
    >>> >>> Performance page in the OpenClinica Wikibook, thinking they would
    >>> >>> dramatically speed up OpenClinica, and your story provides further
    >>> >>> confirmation of it (OpenClinica's Optimized(tm) Hosting uses hybrid
    >>> >>> disks that use SSDs):
    >>>> >>>>
    >>>> >>>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance
    >>>> >>>> "Disk requirements: Whilst the space taken up for the application
    >>>> >>>> and
    >>> >>> PostgreSQL are relatively small (Oracle's requirements will vary),
    >>> >>> faster disks, including SSDs (solid state disks) and high speed hard
    >>> >>> disks, will speed up the response times of PostgreSQL or Oracle. For
    >>> >>> example, OpenClinica Optimized(tm) Hosting (Clinical Trials in the
    >>> >>> Cloud) uses Fusion-io's hybrid disk technology to improve database
    >>> >>> performance.
    >>> >>> Additionally, one user reported faster performance on the
    >>> >>> OpenClinica user list."
    >>>> >>>>
    >>>> >>>> If others are thinking about using SSDs, they should be aware that,
    >>>> >>>> just
    >>> >>> like regular hard drives, SSDs do fail
    >>> >>> (http://www.tomshardware.com/reviews/ssd-reliability-failure-rate,29
    >>> >>> 23.html) , and should be backed up regularly and use RAID where
    >>> >>> appropriate (as with regular hard drives).
    >>>> >>>>
    >>>> >>>> May and Cuneyt, were your versions of OpenClinica upgrades, or
    >>>> >>>> fresh
    >>> >>> installs? There was a fix for 404's and some consolidation of CSS
    >>> >>> that should have sped up 3.1.2 a little (mentioned on
    >>> >>> http://en.wikibooks.org/wiki/OpenClinica_User_Manual/PageAnalysis).
    >>>> >>>>
    >>>> >>>> Yours,
    >>>> >>>>
    >>>> >>>> Michael
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>> >>> On Behalf Of Krister Kristianson
    >>>> >>>> Sent: 30 January 2012 13:40
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> A trick that I been very successful with is to put the database on
    >>>> >>>> a SSD
    >>> >>> drive. What took up to 10 seconds now takes less than 1 second using
    >>> >>> 3.1.2
    >>>> >>>>
    >>>> >>>> Regards
    >>>> >>>>
    >>>> >>>> Krister
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Xi, Xuemei
    >>>> >>>> Sent: 30 January 2012 14:29
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> We have OC3.1.1 and OC3.1.2 instances. We experience that OC3.1.2
    >>>> >>>> is
    >>> >>> slower to load the page than OC3.1.1
    >>>> >>>>
    >>>> >>>> Thanks
    >>>> >>>> May
    >>>> >>>>
    >>>> >>>> -----Original Message-----
    >>>> >>>>
    >>>> >>>> [mailto:[email protected]]
    >>>> >>>> On Behalf Of Cuneyt Parlayan
    >>>> >>>> Sent: Monday, January 30, 2012 3:30 AM
    >>>> >>>> To: [email protected]
    >>>> >>>> Subject: [Users] Performance issues in OpenClinica 3.1.2
    >>>> >>>>
    >>>> >>>> Hi all,
    >>>> >>>>
    >>>> >>>> We are having some performance problems in 3.1.2 which was not the
    >>>> >>>> case in
    >>> >>> earlier versions.
    >>>> >>>>
    >>>> >>>> When data is entered, it takes ± 5 seconds to open the window and
    >>> >>> another
    >>>> >>>> 5 seconds to save the data.
    >>>> >>>> This was not the case before.
    >>>> >>>> Anyone else experiencing this?
    >>>> >>>> Thanks, Cuneyt.
    >>>> >>>>
    >>>> >>>> --
    >>>> >>>> Cuneyt Parlayan
    >>>> >>>>
    >>>> >>>> Datamanager
    >>>> >>>> Department of Pathology
    >>>> >>>> VU University Medical Center
    >>>> >>>> Amsterdam - The Netherlands
    >>>> >>>>
This discussion has been closed.