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Performance issues in OpenClinica 3.1.2

13

Comments

  • kristiakkristiak Posts: 1,329 ✭✭✭
    Hi May,
    I have now tested your two CRF pages on an old "tired" Thinkpad Z61 with 2Gb
    RAM running 64bit WIN7 prof, OC 3.1.2. A pretty tired hard disk as well
    5400 rpm.
    My results were as follows:
    1) Loading the first page 2.4 seconds
    2) Loading the second page < 1 second
    3) Saving page 1 with one record 4.9 seconds
    4 Saving page 2 with two records 3.0 seconds
    This in my book is fully acceptable. Mind you that there is no network
    slowing it down and no other traffic then OC.
    On a powerful server this performance will improve.
    I would, though, try to clean up the first page. Maybe you could divide it
    in two pages as it becomes a little cumbersome to scroll the page.
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 15:21
    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-----
    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
    >>>> >>>>
  • kristiakkristiak Posts: 1,329 ✭✭✭
    Hi May,
    Have configured the TOMCAT properly? With the JAVA options:
    -XX:MaxPermSize=180m and the Maximum memory pool to 1280 Mb?
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 15:02
    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-----
    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-----
    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
    >>>> >>>>
  • mx8866mx8866 Posts: 109
    Hi Krister,
    Thank you so so much for spending time to test the CRFs. I have set Tomcat JAVA Options:
    -XX:MaxPermSize=180m and the Maximum memory pool to 1280 Mb.
    I am thinking to break the first section into 2 sections. But these data are in the same Time Point and Location. Do I have to repeat "Date", "Time" and "Location" in SECTION 2 group if they have filled out in the
    1st section? Do these fields carry over from one section to another section, so the user do not need to input these data again?
    Many many thanks for your helping and advice
    May
    -----Original Message-----
    Sent: Tuesday, January 31, 2012 10:54 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi May,
    Have configured the TOMCAT properly? With the JAVA options:
    -XX:MaxPermSize=180m and the Maximum memory pool to 1280 Mb?
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 15:02
    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-----
    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-----
    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
    >>>> >>>>
  • kristiakkristiak Posts: 1,329 ✭✭✭
    Hi May,
    It is always interesting work with different people and different problems.
    I used to work for Merck & Co Inc for 35 years in Clinical Development in
    several countries including 10 years in the USA.
    About your question: You could set the time and date for the entire group
    and use these time/date points for every value during the data export. I'm
    not exactly sure how the data hangs together so I feel incompetent to help
    you,
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 18:27
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi Krister,
    Thank you so so much for spending time to test the CRFs. I have set Tomcat
    JAVA Options:
    -XX:MaxPermSize=180m and the Maximum memory pool to 1280 Mb.
    I am thinking to break the first section into 2 sections. But these data are
    in the same Time Point and Location. Do I have to repeat "Date", "Time" and
    "Location" in SECTION 2 group if they have filled out in the 1st section?
    Do these fields carry over from one section to another section, so the user
    do not need to input these data again?
    Many many thanks for your helping and advice May
    -----Original Message-----
    On Behalf Of Krister Kristianson
    Sent: Tuesday, January 31, 2012 10:54 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Hi May,
    Have configured the TOMCAT properly? With the JAVA options:
    -XX:MaxPermSize=180m and the Maximum memory pool to 1280 Mb?
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Xi, Xuemei
    Sent: 31 January 2012 15:02
    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-----
    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-----
    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
    >>>> >>>>
  • Dear Cuneyt,
    As further evidence of the benefits of SSDs. 'dannyl' reported a 2.5-3.0x speed improvement, where using SSDs ' has dropped response time to about 8-10s instead of 20-30s'.
    https://issuetracker.openclinica.com/view.php?id=12197#c42215
    dannyl's bug is one of a couple of performance bugs that appear to be being looked into right now (these may result in a software patch at some point):
    https://issuetracker.openclinica.com/view.php?id=12197
    https://issuetracker.openclinica.com/view.php?id=12979
    (I've added this example of SSD benefits to the Performance page in the Wikibook http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance#The_theory)
    Yours,
    Michael
    -----Original Message-----
    Sent: 31 January 2012 09:29
    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
    >> >>
  • ccollinsccollins Posts: 379 admin
    Michael,
    Yes, Doug and Pradnya are looking into the issue right now. We'll be
    providing our analysis, updates, and plans on issue #12979.
    To summarize it succinctly:
    There are a lot of things you can do to get the most
    performance/scalability/load handling out of OpenClinica. This thread
    and the community resources do a great job of describing many of these
    strategies. There are also a lot of improvements that can be made to the
    software in this area. Identifying and implementing these improvements
    is a priority for us right now and I look forward to sharing these
    improvements in upcoming releases.
    Best,
    Cal
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Michael Bluett
    Sent: Thursday, February 02, 2012 5:16 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Dear Cuneyt,
    As further evidence of the benefits of SSDs. 'dannyl' reported a
    2.5-3.0x speed improvement, where using SSDs ' has dropped response time
    to about 8-10s instead of 20-30s'.
    https://issuetracker.openclinica.com/view.php?id=12197#c42215
    dannyl's bug is one of a couple of performance bugs that appear to be
    being looked into right now (these may result in a software patch at
    some point):
    https://issuetracker.openclinica.com/view.php?id=12197
    https://issuetracker.openclinica.com/view.php?id=12979
    (I've added this example of SSD benefits to the Performance page in the
    Wikibook
    http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance#The_the
    ory)
    Yours,
    Michael
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Cuneyt Parlayan
    Sent: 31 January 2012 09:29
    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]rg
    > > 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: 1,329 ✭✭✭
    Hi Cal,
    With the risk of upsetting many Linux fans I can contribute this piece of
    information. Having a long experience from HP Unix and Oracle it seemed
    natural for us to run Linux (Ubuntu) when we started to use OC. XP and Vista
    were really no valid choices. However, when WINDOWS 7 came along we were
    surprised over the performance improvement over Ubuntu, this was also the
    case for Windows 2008 R2 server. Ever since we have switched to the WINDOWS
    environment 100% and are very happy with the choice.
    A number of inflamed articles have been written about this subject and I
    will only quote one of the most elaborate tests I have been able to dig up:
    http://www.phoronix.com/scan.php?page=article&item=linux_windows_part1&num=1
    Although this article takes mainly about gaming it has a lot of valuable
    comments.
    Thus, when talking about performance I think it is important to also focus
    on the operating system.
    In conclusion: In our experience running powerful servers and desktops with
    lots of memory and SSD drives we have so far not discovered any performance
    issues with OpenClinica 3.1.2.
    Regards
    Krister
    -----Original Message-----
    On Behalf Of Cal Collins
    Sent: 03 February 2012 00:04
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Michael,
    Yes, Doug and Pradnya are looking into the issue right now. We'll be
    providing our analysis, updates, and plans on issue #12979.
    To summarize it succinctly:
    There are a lot of things you can do to get the most
    performance/scalability/load handling out of OpenClinica. This thread and
    the community resources do a great job of describing many of these
    strategies. There are also a lot of improvements that can be made to the
    software in this area. Identifying and implementing these improvements is a
    priority for us right now and I look forward to sharing these improvements
    in upcoming releases.
    Best,
    Cal
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Michael Bluett
    Sent: Thursday, February 02, 2012 5:16 AM
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2
    Dear Cuneyt,
    As further evidence of the benefits of SSDs. 'dannyl' reported a 2.5-3.0x
    speed improvement, where using SSDs ' has dropped response time to about
    8-10s instead of 20-30s'.
    https://issuetracker.openclinica.com/view.php?id=12197#c42215
    dannyl's bug is one of a couple of performance bugs that appear to be being
    looked into right now (these may result in a software patch at some point):
    https://issuetracker.openclinica.com/view.php?id=12197
    https://issuetracker.openclinica.com/view.php?id=12979
    (I've added this example of SSD benefits to the Performance page in the
    Wikibook
    http://en.wikibooks.org/wiki/OpenClinica_User_Manual/Performance#The_the
    ory)
    Yours,
    Michael
    -----Original Message-----
    [mailto:[email protected]] On Behalf Of Cuneyt Parlayan
    Sent: 31 January 2012 09:29
    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
    >> >>
  • On Friday, February 03, 2012 10:31:31 AM Krister Kristianson wrote:
    > Hi Cal,
    >
    > With the risk of upsetting many Linux fans I can contribute this piece of
    > information. Having a long experience from HP Unix and Oracle it seemed
    > natural for us to run Linux (Ubuntu) when we started to use OC. XP and Vista
    > were really no valid choices. However, when WINDOWS 7 came along we were
    > surprised over the performance improvement over Ubuntu, this was also the
    > case for Windows 2008 R2 server. Ever since we have switched to the WINDOWS
    > environment 100% and are very happy with the choice.
    >
    > A number of inflamed articles have been written about this subject and I
    > will only quote one of the most elaborate tests I have been able to dig up:
    > http://www.phoronix.com/scan.php?page=article&item=linux_windows_part1&num=1
    > Although this article takes mainly about gaming it has a lot of valuable
    > comments.
    >
    > Thus, when talking about performance I think it is important to also focus
    > on the operating system.
    >
    > In conclusion: In our experience running powerful servers and desktops with
    > lots of memory and SSD drives we have so far not discovered any performance
    > issues with OpenClinica 3.1.2.
    >

    A while back I would have disagreed. However it looks like Windows 7 is finally able to deliver what GNU/Linux has for a long time. Given the company backing we are now in an era where competition is about features (such as performance and stability) rather then ideologies.

    One benefit of GNU/Linux remains however. Just in case anything goes wrong you have at least a chance to debug while on Windows you more often then not do not.

    In a era of SaaS the customer could not care less as long as OC does what it is supposed to and does it fast.

    Regards,
    Sebastian Hilbert
  • kristiakkristiak Posts: 1,329 ✭✭✭
    Agree Sebastian, but on the other hand Windows Server 2008 R2 or SBS are extremely stable version of Windows. We have been running these + Windows 7 for several years now and have not had an operating system related problem once since!

    Regards

    Krister
    Sent: 03 February 2012 11:35
    To: [email protected]
    Subject: Re: [Users] Performance issues in OpenClinica 3.1.2

    On Friday, February 03, 2012 10:31:31 AM Krister Kristianson wrote:
    > Hi Cal,
    >
    > With the risk of upsetting many Linux fans I can contribute this piece of
    > information. Having a long experience from HP Unix and Oracle it seemed
    > natural for us to run Linux (Ubuntu) when we started to use OC. XP and Vista
    > were really no valid choices. However, when WINDOWS 7 came along we were
    > surprised over the performance improvement over Ubuntu, this was also the
    > case for Windows 2008 R2 server. Ever since we have switched to the WINDOWS
    > environment 100% and are very happy with the choice.
    >
    > A number of inflamed articles have been written about this subject and I
    > will only quote one of the most elaborate tests I have been able to dig up:
    > http://www.phoronix.com/scan.php?page=article&item=linux_windows_part1&num=1
    > Although this article takes mainly about gaming it has a lot of valuable
    > comments.
    >
    > Thus, when talking about performance I think it is important to also focus
    > on the operating system.
    >
    > In conclusion: In our experience running powerful servers and desktops with
    > lots of memory and SSD drives we have so far not discovered any performance
    > issues with OpenClinica 3.1.2.
    >

    A while back I would have disagreed. However it looks like Windows 7 is finally able to deliver what GNU/Linux has for a long time. Given the company backing we are now in an era where competition is about features (such as performance and stability) rather then ideologies.

    One benefit of GNU/Linux remains however. Just in case anything goes wrong you have at least a chance to debug while on Windows you more often then not do not.

    In a era of SaaS the customer could not care less as long as OC does what it is supposed to and does it fast.

    Regards,
    Sebastian Hilbert
  • kristiakkristiak Posts: 1,329 ✭✭✭
    Hi May,
    I have loaded your form on a much faster device and tested it with 20
    patients. The performance was still excellent. The form opened in about 1
    second and saved in 4-5 seconds regardless of 1 or 20 patients.
    Have you had a chance to redesign the form yet? I have looked into it but
    it is difficult when you have not seen the protocol. But first of all I
    would try to get rid of the division of form 1 in two depending on the
    selection of Other Location. The I would make each day a separate event,
    that mean that you could skip the date for each record....would that work?
    But as I said I'm not sure as I said. How many days is the study with these
    recording going to continue.
    Best regards
    Krister
    -----Original Message-----
    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-----
    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.