[gradsusr] Performance issue with large files open
Brian Gaze
brianw.gaze at googlemail.com
Thu Feb 14 04:19:50 EST 2019
>The number of open files should not affect performance. How many files are
you talking >about? What kind of aggregation? Can you document the
performance change so it can be >reproduced?
General scenario and ballpark figures:
Concatenate (and regrid as necessary) GFS / GEFS grib files for all
perturbations as well as the control, mean and operational run to produce
23 files containing time steps from 0 to 384 hours.
1) Run .gs to produce line graphs which plot 2 variables for each run (e.g.
850hPa temps and MSLP)
In this case it takes a number of seconds to generate one chart (between 4
to 7 secs depending on the processor speed and version of Grads - the
latest Linux version appears to be a little quicker than OpenGrads on
Windows).
2) Plot only one variable (e.g. 850hPa temps) for each run
In this case several charts per second are generated.
Sorry I can't give more precise metrics at the moment.
Thanks
BWG
On Wed, 13 Feb 2019 at 00:49, <gradsusr-request at gradsusr.org> wrote:
> Send gradsusr mailing list submissions to
> gradsusr at gradsusr.org
>
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> or, via email, send a message with subject or body 'help' to
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>
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> than "Re: Contents of gradsusr digest..."
>
>
> Today's Topics:
>
> 1. Running GrADS in Windows (10 x64) - IS POSSIBLE! (without
> OpenGrads) (Netanel_H)
> 2. Running GrADS in Windows (10 x64) - IS POSSIBLE! (without
> OpenGrads) - second try (Netanel_H)
> 3. Re: Performance issue with large files open (was: Problem
> with Nomads servers) (Jennifer M Adams)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 12 Feb 2019 22:45:17 +0200
> From: Netanel_H <netanel at gmx.com>
> To: gradsusr at gradsusr.org
> Subject: [gradsusr] Running GrADS in Windows (10 x64) - IS POSSIBLE!
> (without OpenGrads)
> Message-ID: <5C63305D.2020706 at gmx.com>
> Content-Type: text/plain; charset="us-ascii"
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 12 Feb 2019 22:50:50 +0200
> From: Netanel_H <netanel at gmx.com>
> To: gradsusr at gradsusr.org
> Subject: [gradsusr] Running GrADS in Windows (10 x64) - IS POSSIBLE!
> (without OpenGrads) - second try
> Message-ID: <5C6331AA.3060304 at gmx.com>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Another try because first came as HTML
>
> Hello everybody,
>
> I just successfully tested WSL (Windows Subsystem for Linux)
> https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux
> for running GrADS and it's working!
>
> Short explanation:
> 1) Install WSL from windows features (reboot)
> 2) Install linux distribution from Windows Store or manual install from
> links here -
> https://docs.microsoft.com/en-us/windows/wsl/install-manual
> (I tested it in Debian)
>
> 3) open wsl.exe (search from it), in Debian it asks to choose
> username/password for the new subsystem
> 4) In the new terminal run: sudo apt-get install grads (asks for the
> password from the previous stage)
> (this command is only for debian/ubuntu, other distributions have others
> command for software packages)
>
> 5) install VcXsrv from here -
> https://sourceforge.net/projects/vcxsrv/
> 6) Run VcXsrv wizard (XLaunch)
>
> 7) In Linux terminal type: nano ~/.bashrc
> 8) Add this 2 lines at the end of file:
> DISPLAY=:0.0
> export DISPLAY
>
> 9) Ctrl+x and answer y (+Enter) for saving modified file
>
> 10) Close Linux Subsystem and open it again
>
> 11) type in terminal: grads
>
> If everything went well, GrADS window will be open
>
> note: in Linux Subsystem Windows C volume is mounted as /mnt/c, D as
> /mnt/d etc. That is the easy way to pass files between Windows and Linux
> Subsystem
>
> Enjoy!
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 12 Feb 2019 23:12:41 +0000
> From: Jennifer M Adams <jadams21 at gmu.edu>
> To: GrADS Users Forum <gradsusr at gradsusr.org>
> Subject: Re: [gradsusr] Performance issue with large files open (was:
> Problem with Nomads servers)
> Message-ID: <26C38886-2D1A-4E56-BB58-48EA759617DA at gmu.edu>
> Content-Type: text/plain; charset="utf-8"
>
>
>
> > On Feb 11, 2019, at 4:48 AM, Brian Gaze <brianw.gaze at googlemail.com>
> wrote:
> >
> > One thing I have noticed with 2.x versions of GrADS and OpenGrADS is
> that they run into performance issues when many large files are opened. An
> example is when working with aggregated GFS / GEFS data sets.
> The number of open files should not affect performance. How many files are
> you talking about? What kind of aggregation? Can you document the
> performance change so it can be reproduced?
>
>
> > I believe this *could* be related to the metabuffer filling up?
> Therefore I wondered whether it would be possible for you to add a command
> line switch that sets the metabuffer size at run time?
> That is already in GrADS:
>
> -m NNN Sets metafile buffer size to NNN, which must be an integer.
> Default value is 1000000.
>
> In more recent versions, the metabuffer is dynamically allocated as
> needed, so the -m argument is not needed and therefore ignored.
>
> ?Jennifer
>
> >
> > Thanks
> >
> > BWG
> >
> >
> >
> >
> > On Mon, 11 Feb 2019 at 08:53, <gradsusr-request at gradsusr.org> wrote:
> > Send gradsusr mailing list submissions to
> > gradsusr at gradsusr.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://gradsusr.org/mailman/listinfo/gradsusr
> > or, via email, send a message with subject or body 'help' to
> > gradsusr-request at gradsusr.org
> >
> > You can reach the person managing the list at
> > gradsusr-owner at gradsusr.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gradsusr digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: problens with opendap from nomads (Reginaldo Ventura de S?)
> > 2. Re: Problem with Nomads servers (Arlindo da Silva)
> > 3. Re: Problem with Nomads servers (Tim Van Damme)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 11 Feb 2019 00:10:59 -0200
> > From: Reginaldo Ventura de S? <regis at lamma.ufrj.br>
> > To: GrADS Users Forum <gradsusr at gradsusr.org>
> > Subject: Re: [gradsusr] problens with opendap from nomads
> > Message-ID:
> > <CADz=
> HLORo_GL+-zZ9mZscGAufBei6zEd7msccRZQrbxwhi7jTA at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > >From NCEP Support.
> > Hello,
> >
> > Yesterday was our cut-over date for NOMADS transition to HTTPS. As we had
> > advertised in our NWS Service Change Notices (SCN) and NOMADS Listserv
> > emails over the last month, users of Opendap would be affected by the
> > transition to HTTPS. This is because most versions of GRADS prior to
> GRADS
> > v2.2.0 do not support SSL (downloading from https websites). You will
> need
> > to download/install a more recent version of GRADS in order to regain
> > access to NOMADS Opendap data feeds.
> >
> > GRADS can be downloaded from the COLA website.
> http://cola.gmu.edu/grads/
> >
> > It is also possible that your version of curl needs to be updated to
> > support SSL.
> >
> > Please let us know if we can be of further assistance.
> >
> > On Wed, Feb 6, 2019 at 4:10 PM Mark Sponsler <msponsler at comcast.net>
> wrote:
> >
> > > Hi,
> > > Yes.
> > > It does not work.
> > > NOAA converted all their DODS servers to https format yesterday. The
> > > latest version of Opengrads does not support https secure connection.
> > >
> > > I've sent a message to the gentleman that supports opengrads to see if
> a
> > > hot fix is in work.
> > >
> > > More to follow.
> > > Thanks,
> > > Mark
> > >
> > > On February 6, 2019 9:47:43 AM PST, "Reginaldo Ventura de S?" <
> > > regis at lamma.ufrj.br> wrote:
> > >>
> > >>
> > >> Dear users,
> > >>
> > >> Is anyone having trouble to acess nomads using opendap?
> > >>
> > >>
> > >> greetings
> > >> []?regis
> > >>
> > >
> > > Thanks,
> > > Mark Sponsler
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> http://gradsusr.org/pipermail/gradsusr/attachments/20190211/bb0bd8a0/attachment-0001.html
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 10 Feb 2019 23:33:47 -0500
> > From: Arlindo da Silva <dasilva at alum.mit.edu>
> > To: tim at stormcell.be, GrADS Users Forum <gradsusr at gradsusr.org>
> > Subject: Re: [gradsusr] Problem with Nomads servers
> > Message-ID:
> > <
> CALz7xZcCoN5yXj+kxesDhGuAHqPsT9km95Wu2mBujNJJyY5i6Q at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > All,
> >
> > OpenGrADS builds for 2.2.1 will be announced soon. They are
> undergoing
> > additional testing. And yes, https:// will be enabled.
> >
> > Arlindo
> >
> >
> > On Sun, Feb 10, 2019 at 6:00 AM Tim Van Damme <tim at stormcell.be> wrote:
> >
> > > I am experiencing the same issue with Opengrads for Windows.
> > >
> > > It would be cool if there would be a simple workaround.
> > >
> > >
> > >
> > > Tim
> > >
> > >
> > >
> > > *From:* gradsusr [mailto:gradsusr-bounces at gradsusr.org] *On Behalf Of
> *avi
> > > kojokro
> > > *Sent:* 10 February 2019 09:39
> > > *To:* GrADS Users Forum <gradsusr at gradsusr.org>
> > > *Subject:* Re: [gradsusr] Problem with Nomads servers
> > >
> > >
> > >
> > > Hi Jennifer
> > >
> > > thank you for the answer
> > > I forgot to mention that I use Grads on windows
> > > Is there a solution to this issue?
> > >
> > >
> > >
> > > Avi.
> > >
> > >
> > >
> > > ??????? ???, 9 ????? 2019 ?-17:50 ??? ?Jennifer M Adams? <?
> > > jadams21 at gmu.edu?>:
> > >
> > > Opengrads builds are not linked with an SSL-enabled version of the curl
> > > library, which means that they are unable to access HTTPS opendap URLs.
> > > Until Arlindo posts new builds, you will have to use COLA?s version of
> > > GrADS, version 2.1.1.b0 or newer.
> > > ?Jennifer
> > >
> > > > On Feb 9, 2019, at 9:43 AM, avi kojokro <kojokroavi at gmail.com>
> wrote:
> > > >
> > > >
> > > > Hello everyone,
> > > > For a few days now, there has been a problem connecting to Nomads
> servers
> > > > Here is a Screenshot of the Grads command board, I tried to enter the
> > > server both with the HTTP address and also with the HTTPS address and
> both
> > > cannot log on to the server, The same problem also for the servers of
> > > preparafv3.......
> > > > Does anyone know what the problem is?.
> > > >
> > > > the Screenshot: for GFS
> > > >
> > > >
> > > > GX Package Initialization: Size = 11 8.5
> > > > Command line history in \Users\OWNER/.grads.log
> > > > <://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > > Scanning self-describing file:
> > > http://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > > curl error details:
> > > > Error: nc_open failed to open file
> > > http://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > > NetCDF: I/O failure
> > > > gadsdf: Couldn't ingest SDF metadata.
> > > > <s://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > > Scanning self-describing file:
> > > https://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > > curl error details:
> > > > Error: nc_open failed to open file
> > > https://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > > NetCDF: I/O failure
> > > > gadsdf: Couldn't ingest SDF metadata.
> > > > ga->
> > > >
> > > > the Screenshot: for preparafv3
> > > >
> > > >
> > > > Command line history in \Users\OWNER/.grads.log
> > > > <090/dods/gfs_0p25_preparafv3/gfs20190208/gfs_0p25_preparafv3_12z
> > > > Scanning self-describing file:
> > >
> https://nomads.ncep.noaa.gov:9090/dods/gfs_0p25_preparafv3/gfs20190208/gfs_0p25_preparafv3_12z
> > > > curl error details:
> > > > Error: nc_open failed to open file
> > >
> https://nomads.ncep.noaa.gov:9090/dods/gfs_0p25_preparafv3/gfs20190208/gfs_0p25_preparafv3_12z
> > > > NetCDF: I/O failure
> > > > gadsdf: Couldn't ingest SDF metadata.
> > > > ga->
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > gradsusr mailing list
> > > > gradsusr at gradsusr.org
> > > >
> > >
> http://secure-web.cisco.com/1YIE5nvA4vDI11pJu6xRoRasU3TtHbb6Nb_ipY6ubaBWg-MrWxXs-Ow4mVOT1fmEMkxfc61JM-vXkeleikdHwg3aqcbNnyt7_L60-pTtRlBbh9kWxwK6NddFFapjPLsum26-wvNlFJgkZBRxlD0CGY3IEI4eTOMrI2IOuCPIVDe9FAlVMm3qI5p4QgnJ_o1LB2pPxTAeZdZr55-dqEUDEhcsiKJRsWYVseFYyyfSWcLJUcw-8J_c_U5YZCjFdAbwn_C1CeooqQsIO7klAy8eQv8J5iUC0rd-j93KIgO5vbva2i7fRVtKXTluWYn8-AeRDRRZqzoEk3sG2GdiMfhgKALBLOPDEx9sW1ZXO3LNCoS3SKOmDmp0xOdsF05J23qtNwlsMt23x9VVaGf1MWOgfcMlmaTC9A6LTUN4ArpIpeShINH26j3bbZGIG30lLAXLD/http%3A%2F%2Fgradsusr.org%2Fmailman%2Flistinfo%2Fgradsusr
> > >
> > > --
> > > Jennifer Miletta Adams
> > > Center for Ocean-Land-Atmosphere Studies (COLA)
> > > George Mason University
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > gradsusr mailing list
> > > gradsusr at gradsusr.org
> > > http://gradsusr.org/mailman/listinfo/gradsusr
> > >
> > > _______________________________________________
> > > gradsusr mailing list
> > > gradsusr at gradsusr.org
> > > http://gradsusr.org/mailman/listinfo/gradsusr
> > >
> >
> >
> > --
> > Arlindo da Silva
> > *dasilva at alum.mit.edu <dasilva at alum.mit.edu>*
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 11 Feb 2019 08:30:17 +0100
> > From: "Tim Van Damme" <tim at stormcell.be>
> > To: "'Arlindo da Silva'" <dasilva at alum.mit.edu>, "'GrADS Users Forum'"
> > <gradsusr at gradsusr.org>
> > Subject: Re: [gradsusr] Problem with Nomads servers
> > Message-ID: <000c01d4c1db$a442d930$ecc88b90$@stormcell.be>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello Arlindo,
> >
> >
> >
> > That is fantastic news. Let?s hope we do not need to alter our scripts
> fort he newer version of Opengrads.
> >
> > Meanwhile I was wondering? if anyone has a GFS script that shows the
> different sorts of precipitation on one map... -> i am interested!
> >
> >
> >
> >
> >
> > Kind regards,
> >
> >
> >
> > Tim
> >
> >
> >
> > From: Arlindo da Silva [mailto:dasilva at alum.mit.edu]
> > Sent: 11 February 2019 05:34
> > To: tim at stormcell.be; GrADS Users Forum <gradsusr at gradsusr.org>
> > Subject: Re: [gradsusr] Problem with Nomads servers
> >
> >
> >
> > All,
> >
> >
> >
> > OpenGrADS builds for 2.2.1 will be announced soon. They are
> undergoing additional testing. And yes, https:// will be enabled.
> >
> >
> >
> > Arlindo
> >
> >
> >
> >
> >
> > On Sun, Feb 10, 2019 at 6:00 AM Tim Van Damme <tim at stormcell.be <mailto:
> tim at stormcell.be> > wrote:
> >
> > I am experiencing the same issue with Opengrads for Windows.
> >
> > It would be cool if there would be a simple workaround.
> >
> >
> >
> > Tim
> >
> >
> >
> > From: gradsusr [mailto:gradsusr-bounces at gradsusr.org <mailto:
> gradsusr-bounces at gradsusr.org> ] On Behalf Of avi kojokro
> > Sent: 10 February 2019 09:39
> > To: GrADS Users Forum <gradsusr at gradsusr.org <mailto:
> gradsusr at gradsusr.org> >
> > Subject: Re: [gradsusr] Problem with Nomads servers
> >
> >
> >
> > Hi Jennifer
> >
> > thank you for the answer
> > I forgot to mention that I use Grads on windows
> > Is there a solution to this issue?
> >
> >
> >
> > Avi.
> >
> >
> >
> > ??????? ???, 9 ????? 2019 ?-17:50 ??? ?Jennifer M Adams? <? <mailto:
> jadams21 at gmu.edu> jadams21 at gmu.edu?>:
> >
> > Opengrads builds are not linked with an SSL-enabled version of the curl
> library, which means that they are unable to access HTTPS opendap URLs.
> > Until Arlindo posts new builds, you will have to use COLA?s version of
> GrADS, version 2.1.1.b0 or newer.
> > ?Jennifer
> >
> > > On Feb 9, 2019, at 9:43 AM, avi kojokro <kojokroavi at gmail.com <mailto:
> kojokroavi at gmail.com> > wrote:
> > >
> > >
> > > Hello everyone,
> > > For a few days now, there has been a problem connecting to Nomads
> servers
> > > Here is a Screenshot of the Grads command board, I tried to enter the
> server both with the HTTP address and also with the HTTPS address and both
> cannot log on to the server, The same problem also for the servers of
> preparafv3.......
> > > Does anyone know what the problem is?.
> > >
> > > the Screenshot: for GFS
> > >
> > >
> > > GX Package Initialization: Size = 11 8.5
> > > Command line history in \Users\OWNER/.grads.log
> > > <://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z <
> http://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z>
> > > Scanning self-describing file:
> http://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > curl error details:
> > > Error: nc_open failed to open file
> http://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > NetCDF: I/O failure
> > > gadsdf: Couldn't ingest SDF metadata.
> > > <s://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z <
> http://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z>
> > > Scanning self-describing file:
> https://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > curl error details:
> > > Error: nc_open failed to open file
> https://nomads.ncep.noaa.gov:80/dods/gfs_0p25/gfs20190209/gfs_0p25_00z
> > > NetCDF: I/O failure
> > > gadsdf: Couldn't ingest SDF metadata.
> > > ga->
> > >
> > > the Screenshot: for preparafv3
> > >
> > >
> > > Command line history in \Users\OWNER/.grads.log
> > > <090/dods/gfs_0p25_preparafv3/gfs20190208/gfs_0p25_preparafv3_12z
> > > Scanning self-describing file:
> https://nomads.ncep.noaa.gov:9090/dods/gfs_0p25_preparafv3/gfs20190208/gfs_0p25_preparafv3_12z
> > > curl error details:
> > > Error: nc_open failed to open file
> https://nomads.ncep.noaa.gov:9090/dods/gfs_0p25_preparafv3/gfs20190208/gfs_0p25_preparafv3_12z
> > > NetCDF: I/O failure
> > > gadsdf: Couldn't ingest SDF metadata.
> > > ga->
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > gradsusr mailing list
> > > gradsusr at gradsusr.org <mailto:gradsusr at gradsusr.org>
> > >
> http://secure-web.cisco.com/1YIE5nvA4vDI11pJu6xRoRasU3TtHbb6Nb_ipY6ubaBWg-MrWxXs-Ow4mVOT1fmEMkxfc61JM-vXkeleikdHwg3aqcbNnyt7_L60-pTtRlBbh9kWxwK6NddFFapjPLsum26-wvNlFJgkZBRxlD0CGY3IEI4eTOMrI2IOuCPIVDe9FAlVMm3qI5p4QgnJ_o1LB2pPxTAeZdZr55-dqEUDEhcsiKJRsWYVseFYyyfSWcLJUcw-8J_c_U5YZCjFdAbwn_C1CeooqQsIO7klAy8eQv8J5iUC0rd-j93KIgO5vbva2i7fRVtKXTluWYn8-AeRDRRZqzoEk3sG2GdiMfhgKALBLOPDEx9sW1ZXO3LNCoS3SKOmDmp0xOdsF05J23qtNwlsMt23x9VVaGf1MWOgfcMlmaTC9A6LTUN4ArpIpeShINH26j3bbZGIG30lLAXLD/http%3A%2F%2Fgradsusr.org%2Fmailman%2Flistinfo%2Fgradsusr
> >
> > --
> > Jennifer Miletta Adams
> > Center for Ocean-Land-Atmosphere Studies (COLA)
> > George Mason University
> >
> >
> >
> >
> > _______________________________________________
> > gradsusr mailing list
> > gradsusr at gradsusr.org <mailto:gradsusr at gradsusr.org>
> > http://gradsusr.org/mailman/listinfo/gradsusr
> >
> > _______________________________________________
> > gradsusr mailing list
> > gradsusr at gradsusr.org <mailto:gradsusr at gradsusr.org>
> > http://gradsusr.org/mailman/listinfo/gradsusr
> >
> >
> >
> >
> >
> >
> > --
> >
> > Arlindo da Silva
> > dasilva at alum.mit.edu <mailto:dasilva at alum.mit.edu>
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> --
> Jennifer Miletta Adams
> Center for Ocean-Land-Atmosphere Studies (COLA)
> George Mason University
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