Re: Slow Lab Loading in Thunder Bay (Oscarmcmaster-bc-users Digest, Vol 121, Issue 21)

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Re: Slow Lab Loading in Thunder Bay (Oscarmcmaster-bc-users Digest, Vol 121, Issue 21)

Dr Jan MacPhail
Re: Daniel Ek's post
As a locum (in a Thunder Bay clinic with a different OSP) I have not encountered significant delays in lab loading. It's comparable to my experience in BC. Remote access is always a bit slower and 100 MP/S helps!  Very happy to see Thunder Bay participating on line. Thank you Peter H-C for your helpful comments, as always.

Jan MacPhail
BC 10651
ON 32059

On Oct 20, 2016, at 08:09, [hidden email] wrote:

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>   1. Re: [Oscarmcmaster-ontario-users] Slow    display of lab reports
>      (Peter Hutten-Czapski)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 19 Oct 2016 20:27:26 -0400
> From: Peter Hutten-Czapski <[hidden email]>
> Subject: Re: [Oscarmcmaster-bc-users] [Oscarmcmaster-ontario-users]
>    Slow    display of lab reports
> To: Daniel Ek <[hidden email]>, The OSCAR BC UserGroup list
>    <[hidden email]>
> Cc: "[hidden email]"
>    <[hidden email]>,
>    [hidden email]
> Message-ID:
>    <CAHNNH=H2T9DvcUQAysOo0hTwn6frhF=[hidden email]>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Daniel
>
> Welcome to OSCAR users list from the other half of Northern Ontario!
>
> Before I add my $0.02 about tuning OSCAR I should mention that the bc list
> is better monitored and is more active... even for Ontario specific issues
> (including lol the Indivica fork) so I have CC'd there
>
> First of all are you slow?
> Oscar naturally has several areas where it can be slow.  The inbox, I
> believe contributed by the same Indivica so they should know it, is often
> the area where this is seen, however chart opening can be slow.
>
> My benchmarks for remote access is 12 seconds for a chart open (albeit a
> chart with 10+ years of OSCAR data filling all the boxes)
> 6 seconds for Inbox to load the list of all new results and HRM reports
> an additional 20 seconds for preview to load for the first time
> and an additional 3 seconds for preview to load the next bunch of reports
> when you reach the end of preview
>
> Tuning OSCAR for speed
> ===================
>
> More or less in increasing orders of complexity.  Take with a grain of salt
> as you are getting this from a physician, and not a systems operator type.
>
> 1) Physical Memory.  If the server is running out of memory then the
> operating system will write memory to hard disk which substantially and
> abruptly slows the server.  Look at Admin > System Reports > System status
> for the box called vmstat
>
> $ vmstat
> procs -----------memory---------- ---swap-- -----io---- -system-- ------cpu-----
> r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa st
> 1  0 697952 974068 516076 21689712    0    0   102   331    3    3 15
> 2 82  1  0
>
> In the above example there is plenty free (for more details google
> vmstat) so this system is not currently running into an issue
>
> But if it was physical memory is cheap and easy to add to your machine
>
> 2) Java Memory allocation to Tomcat Even if you have lots of physical
> memory if Java is not allowed to use it it will start using the hard
> drive with the same symptoms.
> Adding memory will not solve this, you have to increase the
> allocation.  There are many ways to determine how much memory Java is
> using.
> In OSCAR 15 enable monitoring (see
> http://oscarmanual.org/15/5.0/monitoring ).  It has lots of
> performance data (including how much Java memory is being used)
>
> on the same well resourced box as in 1) the data is currently as below
> Java memory used: 746 Mb / 7,897 Mb
>
> Its fine (at this time)  However if it wasn't adjust this in
> /etc/default/tomcat6
> (for OSCAR 15 its in /etc/default/tomcat7)
>
> As a rule of thumb (if you lack this data) ensure that a good 60% -
> 70% of physical memory is allocated to Java.
>
> 3) MySQL itself.  There are books on tuning it but for most you can
> run a tool called mysql tuner Simply.
> apt-get install
> *mysqltuner *The script will analyse your MySQL instance and suggest
> settings for  /etc/mysql/my.cnf
>
> 4) Oscar indices.  As in a library databases use indexes to quicky
> find the information you want.
>
> You can determine if the queries are running quickly by using the
> monitoring tool. Any query running more than half a second (500ms) is
> noticable to the end user.
> Some time has been spent in OSCAR 15 to optimise indices but I still
> have the following SQL which takes about a second to run
>
> select hl7textinf0_.id as id332_, hl7textinf0_.accessionNum as
> accessio2_332_, hl7textinf0_.discipline as discipline332_,
> hl7textinf0_.filler_order_num as filler4_332_,
> hl7textinf0_.final_result_count as final5_332_, hl7textinf0_.first_name
> as first6_332_, hl7textinf0_.health_no as health7_332_,
> hl7textinf0_.lab_no as lab8_332_, hl7textinf0_.label as label332_,
> hl7textinf0_.last_name as last10_332_, hl7textinf0_.obr_date as
> obr11_332_, hl7textinf0_.priorSimply.ity as priority332_,
> hl7textinf0_.report_status as report13_332_,
> hl7textinf0_.requesting_client as requesting14_332_,
> hl7textinf0_.result_status as result15_332_,
> hl7textinf0_.sending_facility as sending16_332_, hl7textinf0_.sex as
> sex332_ from hl7TextInfo hl7textinf0_ where hl7textinf0_.accessionNum
> like ?
>
> Java Melody Monitoring advises that its run in /lab/newLabUpload.do
> I don't care about a one second wait, and this is not your problem anyway
>
> If you lack this monitoring tool you may activate the slow query log of
> mysql in /etc/mysql/my.cnf by adding the following
>
> long_query_time=2
> log-slow-queries=/var/log/mysql/log-slow-queries.log
> log-queries-not-using-indexes
>
> Note that the slow-log itself can slow performance.  Turn it off when you
> are not using it!
> 5) A bigger faster box.  This is so rarely the issue that I hesitate to
> suggest it.  However if you are big enough (number of users say > 100)
> MySQL starts slowing down.  The real symptom of this is that people start
> volunteering for evening shifts so that they can get through their inboxes
> quickly.
>
> You should only consider a bigger box(s) after you have exhausted the
> above.  In those cases there are ways to split off the OSCAR server(s) from
> multiple MySQL (or MariaDB) servers that load balance.  This is so over my
> head and experience that I shudder at contemplating this solution.
>
>
> ================
> Peter Hutten-Czapski
> Haileybury Ontario
>
> "The attitude that ?if rural people want these services they?ll have to
> come to the city to get them? is simply not acceptable?? (Newbery, 1999)
>
> Before printing, think about the environment. Avant d' imprimer, pensez ?
> l'environnement.
>
>> On 19 October 2016 at 12:55, Daniel Ek <[hidden email]> wrote:
>>
>> Can anyone provide advice on the problem of intermittently having issues
>> with extremely slow  display of lab reports. These are HL-7 files I believe
>> which are received from our hospital and from Lifelabs. They populate the
>> Inbox of OSCAR (version 12.1) and when clicking to view, can take more than
>> a minute to display, and at times the "system" will "time out" and fail to
>> display. This happens whether one is accessing from the Lab file of the
>> patient e-chart, or from our individual Inboxes.
>>
>> This does not happen with Documents which are reports scanned into OSCAR.
>>
>> There is some correlation with the time it takes to open and the length of
>> the report, but frequently one is unable to open a simple lab test of one
>> line only (ex. random glucose). I have had some success by clicking on
>> other lab results in quick succession, and eventually one will open. And
>> sometimes by returning to the original which did not open, it will open
>> unexpectedly quickly.
>>
>> I do not know anything about the server we currently use. Our OSP is
>> Indivica, and they cannot define a specific reason for the problem, as it
>> is not consistent.
>>
>> Dan Ek
>> ------------------------------------------------------------
>> ------------------
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