[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
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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
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> http://lists.einsteintoolkit.org/mailman/listinfo/users
> or, via email, send a message with
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> users-request at einsteintoolkit.org
>
> You can reach the person managing
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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
> (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
>>
>>
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>
> ------------------------------
>
> 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
>>>
>>>
>>
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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
>>
>>
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>
>
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> 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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