[Users] Users Digest, Vol 89, Issue 5

Mikael Sahrling msahrling at yahoo.com
Fri Aug 11 03:31:17 CDT 2017


I did some small edits of the single linux box documentation regarding the local machine specific settings and where to find it.

Mikael

--------------------------------------------
On Thu, 8/10/17,  <users-request at einsteintoolkit.org> wrote:

 Subject: Users Digest, Vol 89, Issue 5
 To: users at einsteintoolkit.org
 Date: Thursday, August 10, 2017, 9:06 PM
 
 Send Users mailing list submissions to
     users at einsteintoolkit.org
 
 To subscribe or unsubscribe via the
 World Wide Web, visit
     http://lists.einsteintoolkit.org/mailman/listinfo/users
 or, via email, send a message with
 subject or body 'help' to
     users-request at einsteintoolkit.org
 
 You can reach the person managing the
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     users-owner at einsteintoolkit.org
 
 When replying, please edit your Subject
 line so it is more specific
 than "Re: Contents of Users digest..."
 
 
 Today's Topics:
 
    1. Re: Changing the default
 directory for simulations (Ian Hinder)
    2. Re: Users Digest, Vol 89,
 Issue 4 (Mikael Sahrling)
    3. wget from google drive
 (Korobkin, Oleg)
    4. Re: Changing the default
 directory for simulations
       (Maitraya
 Bhattacharyya)
 
 
 ----------------------------------------------------------------------
 
 Message: 1
 Date: Thu, 10 Aug 2017 13:58:16 -0500
 From: Ian Hinder <ian.hinder at aei.mpg.de>
 Subject: Re: [Users] Changing the
 default directory for simulations
 To: Maitraya Bhattacharyya <maitraya.linux at gmail.com>
 Cc: Einstein Toolkit Users <users at einsteintoolkit.org>
 Message-ID: <5FA1EF9E-A2B7-4F51-8BF4-6DE3A7819133 at aei.mpg.de>
 Content-Type: text/plain;
 charset="us-ascii"
 
 
 On 10 Aug 2017, at 12:29, Maitraya
 Bhattacharyya <maitraya.linux at gmail.com>
 wrote:
 
 > Hi Ian,
 > 
 > I noticed that there is a
 CESSI-BEAST.ini. I have 24 cores on my machine, I did the
 following changes,
 > 
 > ppn       
      = 256
 > max-num-threads = 256
 > num-threads     = 24
 > nodes       
    = 1
 
 Hi,
 
 The terminology in simfactory is
 confusing, because it is quite old, and the meaning of some
 commonly-used terms has changed.  The full details of
 what everything means are at
 http://simfactory.org/info/documentation/userguide/processterminology.html.
 
 Do you really have 24 physical cores,
 or do you have a processor with 24 hyperthreads on 12
 cores?  If Linux reports 24 cores, then if you have
 hyperthreading, you likely only have 12 cores. 
 
 Can you post the output of "lscpu"?
 
 -- 
 Ian Hinder
 http://members.aei.mpg.de/ianhin
 
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 ------------------------------
 
 Message: 2
 Date: Thu, 10 Aug 2017 13:35:02 -0700
 From: Mikael Sahrling <msahrling at yahoo.com>
 Subject: Re: [Users] Users Digest, Vol
 89, Issue 4
 To: users at einsteintoolkit.org
 Message-ID: <25BFCAC2-F134-4BC5-ABFC-94C02334A41A at yahoo.com>
 Content-Type:
 text/plain;    charset=us-ascii
 
 We should probably update the
 documentation to reflect where the machine specific info is,
 along the lines Ian points out.
 
 I can give it a shot!
 
 Mikael 
 
 Sent from my iPhone
 
 > On Aug 10, 2017, at 10:56 AM, users-request at einsteintoolkit.org
 wrote:
 > 
 > Send Users mailing list
 submissions to
 >    users at einsteintoolkit.org
 > 
 > To subscribe or unsubscribe via
 the World Wide Web, visit
 >    http://lists.einsteintoolkit.org/mailman/listinfo/users
 > or, via email, send a message with
 subject or body 'help' to
 >    users-request at einsteintoolkit.org
 > 
 > You can reach the person managing
 the list at
 >    users-owner at einsteintoolkit.org
 > 
 > When replying, please edit your
 Subject line so it is more specific
 > than "Re: Contents of Users
 digest..."
 > 
 > 
 > Today's Topics:
 > 
 >   1. Re: Changing the default
 directory for simulations
 >      (Maitraya
 Bhattacharyya)
 >   2. Re: Changing the default
 directory for simulations
 >      (Maitraya
 Bhattacharyya)
 >   3. Re: Changing the default
 directory for simulations
 >      (Maitraya
 Bhattacharyya)
 > 
 > 
 >
 ----------------------------------------------------------------------
 > 
 > Message: 1
 > Date: Thu, 10 Aug 2017 22:02:05
 +0530
 > From: Maitraya Bhattacharyya
 <maitraya.linux at gmail.com>
 > Subject: Re: [Users] Changing the
 default directory for simulations
 > To: Ian Hinder <ian.hinder at aei.mpg.de>
 > Cc: Einstein Toolkit Users <users at einsteintoolkit.org>
 > Message-ID:
 >    <CAF9cbAT_YGj-vZCu5_mJuJQ-ocz68vzUvQQJgtAsazQaLWcDGg at mail.gmail.com>
 > Content-Type: text/plain;
 charset="utf-8"
 > 
 > Hi Ian,
 > 
 > Sorry! I forgot to reply to all.
 > 
 > My symfactory defs.local.ini is:
 > 
 > 
 > [default]
 > user       
     = mkb14ip002
 > email       
    = mkb14ip002
 > allocation      =
 NO_ALLOCATION
 > 
 > [CESSI-BEAST]
 > user       
     = mkb14ip002
 > email       
    = mkb14ip002
 > allocation      =
 NO_ALLOCATION
 > basedir     =
 /disk1/maitraya/Einstein_Toolkit/ET_Simulations
 > 
 > My machine is CESSI-BEAST,
 something that I added later for basedir to work.
 > 
 > The command I typed was: 
 ./simfactory/bin/sim submit static_tov
 > --parfile=par/static_tov.par
 --procs=20 --walltime=8:0:0
 > 
 > And the output:
 > Warning: simulation "static_tov"
 does not exist or is not readable
 > Parameter file:
 /disk1/maitraya/Einstein_Toolkit/Cactus/par/static_tov.par
 > Skeleton Created
 > Job directory:
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov"
 > Executable:
 "/disk1/maitraya/Einstein_Toolkit/Cactus/exe/cactus_sim"
 > Option list:
 >
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/SIMFACTORY/cfg/OptionList"
 > Submit script:
 >
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/SIMFACTORY/run/SubmitScript"
 > Run script:
 >
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/SIMFACTORY/run/RunScript"
 > Parameter file:
 >
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/SIMFACTORY/par/static_tov.par"
 > Assigned restart id: 0
 > Error: Too many nodes specified:
 nodes=20 (maxnodes is 1)
 > Aborting Simfactory.
 > 
 > Thanks,
 > Maitraya.
 > 
 > 
 >> On Thu, Aug 10, 2017 at 9:49
 PM, Ian Hinder <ian.hinder at aei.mpg.de>
 wrote:
 >> 
 >> 
 >> On 10 Aug 2017, at 11:08,
 Maitraya Bhattacharyya <maitraya.linux at gmail.com>
 >> wrote:
 >> 
 >> Hi Ian,
 >> 
 >> I have got the basedir to
 work, but I cannot seem to change procs=1
 >> 
 >> Error: Too many nodes
 specified: nodes=20 (maxnodes is 1)
 >> Aborting Simfactory.
 >> 
 >> When I used ubuntu.in, the ppn
 there was set to 256.
 >> 
 >> 
 >> Hi,
 >> 
 >> (Please reply also to the list
 so that other can benefit.  I have re-added
 >> users at einsteintoolkit.org
 to the CC.)
 >> 
 >> Can you post:
 >> 
 >> 1. The command that you typed
 and the error message
 >> 2. The content of
 defs.local.ini
 >> 3. The machine definition for
 the machine you are using
 >> 
 >> I assume you are trying now to
 use ubuntu.ini?
 >> 
 >> --
 >> Ian Hinder
 >> http://members.aei.mpg.de/ianhin
 >> 
 >> 
 > -------------- next part
 --------------
 > An HTML attachment was
 scrubbed...
 > URL: http://lists.einsteintoolkit.org/pipermail/users/attachments/20170810/f99d202a/attachment-0001.html
 
 > 
 > ------------------------------
 > 
 > Message: 2
 > Date: Thu, 10 Aug 2017 22:59:31
 +0530
 > From: Maitraya Bhattacharyya
 <maitraya.linux at gmail.com>
 > Subject: Re: [Users] Changing the
 default directory for simulations
 > To: Ian Hinder <ian.hinder at aei.mpg.de>
 > Cc: Einstein Toolkit Users <users at einsteintoolkit.org>
 > Message-ID:
 >   
 <CAF9cbASELwBeNQo2=487dpVbwsU_zVBbqui+LtJYkvZmAe5inw at mail.gmail.com>
 > Content-Type: text/plain;
 charset="utf-8"
 > 
 > Hi Ian,
 > 
 > I noticed that there is a
 CESSI-BEAST.ini. I have 24 cores on my machine, I
 > did the following changes,
 > 
 > ppn       
      = 256
 > max-num-threads = 256
 > num-threads     = 24
 > nodes       
    = 1
 > 
 > While running, I see the
 following:
 > 
 > + set -e
 > + cd
 >
 /disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/output-0000-active
 > + echo Checking:
 > + pwd
 > + hostname
 > + date
 > + echo Environment:
 > + export CACTUS_NUM_PROCS=1
 > + CACTUS_NUM_PROCS=1
 > + export CACTUS_NUM_THREADS=24
 > + CACTUS_NUM_THREADS=24
 > + export GMON_OUT_PREFIX=gmon.out
 > + GMON_OUT_PREFIX=gmon.out
 > + export OMP_NUM_THREADS=24
 > + OMP_NUM_THREADS=24
 > + env
 > + echo Starting:
 > ++ date +%s
 > + export
 CACTUS_STARTTIME=1502385989
 > + CACTUS_STARTTIME=1502385989
 > + mpirun -np 1
 >
 /disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/SIMFACTORY/exe/cactus_sim
 > -L 3
 >
 /disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/output-0000/static_tov.par
 > 
 > I want to get the -np of the
 mpirun command to be 24. How do I achieve this
 > ?
 > 
 > Maitraya.
 > 
 > On Thu, Aug 10, 2017 at 10:21 PM,
 Maitraya Bhattacharyya <
 > maitraya.linux at gmail.com>
 wrote:
 > 
 >> Hi,
 >> 
 >> There isn't one, so I assume
 that I will have to create one ?
 >> 
 >> Maitraya.
 >> 
 >> On Thu, Aug 10, 2017 at 10:09
 PM, Ian Hinder <ian.hinder at aei.mpg.de>
 >> wrote:
 >> 
 >>> 
 >>> On 10 Aug 2017, at 11:32,
 Maitraya Bhattacharyya <
 >>> maitraya.linux at gmail.com>
 wrote:
 >>> 
 >>> Hi Ian,
 >>> 
 >>> Sorry! I forgot to reply
 to all.
 >>> 
 >>> My symfactory
 defs.local.ini is:
 >>> 
 >>> 
 >>> [default]
 >>> user     
       = mkb14ip002
 >>> email     
      = mkb14ip002
 >>> allocation   
   = NO_ALLOCATION
 >>> 
 >>> [CESSI-BEAST]
 >>> user     
       = mkb14ip002
 >>> email     
      = mkb14ip002
 >>> allocation   
   = NO_ALLOCATION
 >>> basedir     =
 /disk1/maitraya/Einstein_Toolkit/ET_Simulations
 >>> 
 >>> My machine is CESSI-BEAST,
 something that I added later for basedir to
 >>> work.
 >>> 
 >>> The command I typed
 was:  ./simfactory/bin/sim submit static_tov
 >>>
 --parfile=par/static_tov.par --procs=20 --walltime=8:0:0
 >>> 
 >>> And the output:
 >>> Warning: simulation
 "static_tov" does not exist or is not readable
 >>> Parameter file:
 /disk1/maitraya/Einstein_Toolk
 >>>
 it/Cactus/par/static_tov.par
 >>> Skeleton Created
 >>> Job directory:
 "/disk1/maitraya/Einstein_Tool
 >>>
 kit/ET_Simulations/static_tov"
 >>> Executable:
 "/disk1/maitraya/Einstein_Toolkit/Cactus/exe/cactus_sim"
 >>> Option list:
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/
 >>>
 SIMFACTORY/cfg/OptionList"
 >>> Submit script:
 "/disk1/maitraya/Einstein_Tool
 >>>
 kit/ET_Simulations/static_tov/SIMFACTORY/run/SubmitScript"
 >>> Run script:
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_tov/
 >>> SIMFACTORY/run/RunScript"
 >>> Parameter file:
 "/disk1/maitraya/Einstein_Tool
 >>>
 kit/ET_Simulations/static_tov/SIMFACTORY/par/static_tov.par"
 >>> Assigned restart id: 0
 >>> Error: Too many nodes
 specified: nodes=20 (maxnodes is 1)
 >>> Aborting Simfactory.
 >>> 
 >>> 
 >>> Please can you post
 simfactory/mdb/machines/CESSI-BEAST.ini?
 >>> 
 >>> You probably want to set
 "ppn = 20" in that file.
 >>> 
 >>> --
 >>> Ian Hinder
 >>> http://members.aei.mpg.de/ianhin
 >>> 
 >>> 
 >> 
 > -------------- next part
 --------------
 > An HTML attachment was
 scrubbed...
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 > 
 > ------------------------------
 > 
 > Message: 3
 > Date: Thu, 10 Aug 2017 22:21:23
 +0530
 > From: Maitraya Bhattacharyya
 <maitraya.linux at gmail.com>
 > Subject: Re: [Users] Changing the
 default directory for simulations
 > To: Ian Hinder <ian.hinder at aei.mpg.de>
 > Cc: Einstein Toolkit Users <users at einsteintoolkit.org>
 > Message-ID:
 >    <CAF9cbAQDPFeWUUKyOLBMNAVs-sjVKnY3vb7W9vhYMSwZO6fJAw at mail.gmail.com>
 > Content-Type: text/plain;
 charset="utf-8"
 > 
 > Hi,
 > 
 > There isn't one, so I assume that
 I will have to create one ?
 > 
 > Maitraya.
 > 
 >> On Thu, Aug 10, 2017 at 10:09
 PM, Ian Hinder <ian.hinder at aei.mpg.de>
 wrote:
 >> 
 >> 
 >> On 10 Aug 2017, at 11:32,
 Maitraya Bhattacharyya <maitraya.linux at gmail.com>
 >> wrote:
 >> 
 >> Hi Ian,
 >> 
 >> Sorry! I forgot to reply to
 all.
 >> 
 >> My symfactory defs.local.ini
 is:
 >> 
 >> 
 >> [default]
 >> user     
       = mkb14ip002
 >> email     
      = mkb14ip002
 >> allocation     
 = NO_ALLOCATION
 >> 
 >> [CESSI-BEAST]
 >> user     
       = mkb14ip002
 >> email     
      = mkb14ip002
 >> allocation     
 = NO_ALLOCATION
 >> basedir     =
 /disk1/maitraya/Einstein_Toolkit/ET_Simulations
 >> 
 >> My machine is CESSI-BEAST,
 something that I added later for basedir to
 >> work.
 >> 
 >> The command I typed was: 
 ./simfactory/bin/sim submit static_tov
 >> --parfile=par/static_tov.par
 --procs=20 --walltime=8:0:0
 >> 
 >> And the output:
 >> Warning: simulation
 "static_tov" does not exist or is not readable
 >> Parameter file:
 /disk1/maitraya/Einstein_Toolkit/Cactus/par/static_tov.par
 >> Skeleton Created
 >> Job directory:
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_
 >> tov"
 >> Executable:
 "/disk1/maitraya/Einstein_Toolkit/Cactus/exe/cactus_sim"
 >> Option list:
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_
 >>
 tov/SIMFACTORY/cfg/OptionList"
 >> Submit script:
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_
 >>
 tov/SIMFACTORY/run/SubmitScript"
 >> Run script:
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_
 >> tov/SIMFACTORY/run/RunScript"
 >> Parameter file:
 "/disk1/maitraya/Einstein_Toolkit/ET_Simulations/static_
 >>
 tov/SIMFACTORY/par/static_tov.par"
 >> Assigned restart id: 0
 >> Error: Too many nodes
 specified: nodes=20 (maxnodes is 1)
 >> Aborting Simfactory.
 >> 
 >> 
 >> Please can you post
 simfactory/mdb/machines/CESSI-BEAST.ini?
 >> 
 >> You probably want to set "ppn
 = 20" in that file.
 >> 
 >> --
 >> Ian Hinder
 >> http://members.aei.mpg.de/ianhin
 >> 
 >> 
 > -------------- next part
 --------------
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 > 
 > ------------------------------
 > 
 >
 _______________________________________________
 > Users mailing list
 > Users at einsteintoolkit.org
 > http://lists.einsteintoolkit.org/mailman/listinfo/users
 > 
 > 
 > End of Users Digest, Vol 89, Issue
 4
 >
 ************************************
 
 
 
 ------------------------------
 
 Message: 3
 Date: Thu, 10 Aug 2017 22:43:38 +0000
 From: "Korobkin, Oleg" <korobkin at lanl.gov>
 Subject: [Users] wget from google
 drive
 To: "users at einsteintoolkit.org"
 <users at einsteintoolkit.org>
 Message-ID: <1502405018426.29739 at lanl.gov>
 Content-Type: text/plain;
 charset="iso-8859-1"
 
 Hi,
 
 There was a question during the
 Einstein Toolkit workshop about problems with downloading
 files from Google Drive with wget. If the file is shared via
 public link, it is not very hard, i.e. you need to specify
 the object ID:
 
    wget -O <file> https://drive.google.com/uc?id=<FILEID>&export=download
 
 where FILEID is a long string which
 shows up in the shared link. E.g.,
  
    wget -O slides.pdf https://drive.google.com/uc?id=0Bxd8DtQy1EODaHRQd19Wd1M3WUU&export=download
 
 also works with curl:
   
   curl -o slides.pdf -L https://drive.google.com/uc?id=0Bxd8DtQy1EODaHRQd19Wd1M3WUU&export=download
 
 This doesn't really work with privately
 shared files.
 
 Hope this helps,
 Cheers,
  - Oleg Korobkin
 
 ------------------------------
 
 Message: 4
 Date: Fri, 11 Aug 2017 00:38:10 +0530
 From: Maitraya Bhattacharyya <maitraya.linux at gmail.com>
 Subject: Re: [Users] Changing the
 default directory for simulations
 To: Ian Hinder <ian.hinder at aei.mpg.de>
 Cc: Einstein Toolkit Users <users at einsteintoolkit.org>
 Message-ID:
    
 <CAF9cbASXgqtp83h=ehn=c7wLOLc=_kkMsV09n0a9QYa_P-oEWw at mail.gmail.com>
 Content-Type: text/plain;
 charset="utf-8"
 
 Hi Ian,
 
 I have 24 physical cores with
 hyperthreading switched off.
 
 Thanks,
 Maitraya.
 
 On Fri, Aug 11, 2017 at 12:28 AM, Ian
 Hinder <ian.hinder at aei.mpg.de>
 wrote:
 
 >
 > On 10 Aug 2017, at 12:29, Maitraya
 Bhattacharyya <maitraya.linux at gmail.com>
 > wrote:
 >
 > Hi Ian,
 >
 > I noticed that there is a
 CESSI-BEAST.ini. I have 24 cores on my machine,
 > I did the following changes,
 >
 > ppn       
      = 256
 > max-num-threads = 256
 > num-threads     = 24
 > nodes       
    = 1
 >
 >
 > Hi,
 >
 > The terminology in simfactory is
 confusing, because it is quite old, and
 > the meaning of some commonly-used
 terms has changed.  The full details of
 > what everything means are at http://simfactory.org/info/
 >
 documentation/userguide/processterminology.html.
 >
 > Do you really have 24 physical
 cores, or do you have a processor with 24
 > hyperthreads on 12 cores?  If
 Linux reports 24 cores, then if you have
 > hyperthreading, you likely only
 have 12 cores.
 >
 > Can you post the output of
 "lscpu"?
 >
 > --
 > Ian Hinder
 > http://members.aei.mpg.de/ianhin
 >
 >
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 ************************************
 


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