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#26 2021-10-11 19:24:02

ing.nicola
Member
Registered: 2017-12-11
Posts: 139

Re: Questions about singularity version of salome_meca 2021

Maybe I will write a little tutorial on this with your permission.

share and enjoy !

Placing pkginfo.py in ...../aster-src/code_aster/  hg error is solved.

Petsc change often of C API so if you want to use mpi version of code_aster with petsc you have to be up to date.

thanks for the tips . I builded 16.0.8 with PETSC:

singularity run --bind /home:/home -w <full_path_image>.sif shell

in singularity:

export HOST=/home/<folder_sif> ( where placed aster-src and sif image)
export TOOLS="/opt/salome_meca/Salome-V2021-s9/tools"
export ASTER_ROOT_MPI="${TOOLS}/Code_aster_16_0_8_mpi"
export ASTER_ROOT_STD="${TOOLS}/Code_aster_16_0_8_std"

cd ${HOST}/aster-src
./waf_mpi configure --prefix=${ASTER_ROOT_MPI} --install-tests --jobs=8
./waf_mpi build  --jobs=8
./waf_mpi install 

cd ${HOST}/aster-src
./waf_std configure --prefix=${ASTER_ROOT_STD} --install-tests --jobs=8
./waf_std build  --jobs=8
./waf_std install 

echo "vers : 16_0_8_mpi:/opt/salome_meca/Salome-V2021-s9/tools/Code_aster_16_0_8_mpi/share/aster" >> ${TOOLS}/Code_aster_frontend-2021001/etc/codeaster/aster
echo "vers : 16_0_8_std:/opt/salome_meca/Salome-V2021-s9/tools/Code_aster_16_0_8_std/share/aster" >> ${TOOLS}/Code_aster_frontend-2021001/etc/codeaster/aster

out of singularity:

singularity run -w --app install <full_path_image>.sif
./name_image

Last edited by ing.nicola (2021-10-11 22:58:46)

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#27 2021-10-11 21:29:04

ing.nicola
Member
Registered: 2017-12-11
Posts: 139

Re: Questions about singularity version of salome_meca 2021

file pkginfo.py attached.


Attachments:
pkginfo.py, Size: 87 B, Downloads: 251

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#28 2021-10-12 08:45:42

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Good morning,

as promised, I repeated the process with the zipped Code Aster sources. Weirdly enough, even with --without-hg everything works now. For the error of yesterday, I blame the hg version of the sources (but I cannot prove that :-) ).

In the evening I will try this on a headless machine (without Graphics Card).

Thank you again, this is great. I summarized this process on my GitHub-page.

Mario.

https: //github.com/emefff/Code-Aster-MPI-in-Singularity-of-SM2021

Last edited by mf (2021-10-12 08:54:46)

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#29 2021-10-12 12:11:04

ing.nicola
Member
Registered: 2017-12-11
Posts: 139

Re: Questions about singularity version of salome_meca 2021

Great job Mario,
good explaned tutorial.

With pkginfo file , in salome meca list, doesn't appears anymore (0.0.1),  but the version you indicated in the pkginfo list wink

Last edited by ing.nicola (2021-10-12 14:26:33)

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#30 2021-10-12 12:22:06

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello,

thank you, all the credit goes out to you. Yes I thought about including that. Maybe I will try in the evening,

Mario.

Last edited by mf (2021-10-12 12:23:08)

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#31 2021-10-13 10:43:57

sameer21101970
Banned
Registered: 2019-09-06
Posts: 354

Re: Questions about singularity version of salome_meca 2021

Dear Mario,

Can you make a Video of Steps to follow in installation.
Your github is perfect but maximum codeaster users are mechanical or civil engineer & not good at computer science, can't understand what is written.

I think, video will be much help.

Also, you mentioned installation without graphic card, lot of students still using codeaster without graphic card on their pc/laptop. much help procedure awaited.

Regards
Sameer

Last edited by sameer21101970 (2021-10-13 10:49:08)

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#32 2021-10-13 12:08:45

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello Sameer,

I am also not a software engineer :-)...

Just copy the commands in the tutorial to your terminal. A video wouldn't be more helpful I guess, because it's all just terminal commands.

Headless system: When you built your container successfully, you just copy the container to another system (of course, singularity must be installed on this system). In my case on a headless server, when you start Salome Meca, it automatically recognises if you have a graphics card or not (it enters software rendering mode).
If you log on to this headless system with ssh, then don't forget the X-server. On the client side you then log on with 'ssh -X user@xxx.yyy.zzz.aaa'. The GUI will be forwarded to your terminal then.

Just dig into it, it is worth it!

Hope that helps,

Mario.

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#33 2021-10-18 21:07:12

ing.nicola
Member
Registered: 2017-12-11
Posts: 139

Re: Questions about singularity version of salome_meca 2021

with the 16 october 2021 update  ... you can install petsc for 15.4.0 .... ( --disable-petcs is no more necessary ).
The mpi prerequisites have been update.

Last edited by ing.nicola (2021-10-18 22:34:14)

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#34 2021-10-19 10:23:13

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello Nicola,

now the container is perfect. I updated the recipe on my GitHub (remove space in link...)

https: //github.com/emefff/Code-Aster-MPI-in-Singularity-of-SM2021

I also updated the container that can be downloaded there,

thanks for the info,

Mario.

Last edited by mf (2021-10-19 10:24:05)

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#35 2021-10-19 13:52:43

sb1966
Member
From: INDIA
Registered: 2015-03-16
Posts: 249

Re: Questions about singularity version of salome_meca 2021

nicola wrote:

with the 16 october 2021 update  ... you can install petsc for 15.4.0 .... ( --disable-petcs is no more necessary ).
The mpi prerequisites have been update.

Thanks a lot for this new version with PETSC enabled.

mf wrote:

I also updated the container that can be downloaded there

Thanks a lot, Mario, for this modified container with CA-mpi. Also lots of thanks for your step-wise tutorial. It's a great contribution to the community. We had struggled a lot for mpi with earlier CA versions. Decision to use container is really a wise one, I feel.

Presently I am downloading your container and waiting eagerly to try it.

Best regards

Sukumar

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#36 2021-10-20 08:15:21

ing.nicola
Member
Registered: 2017-12-11
Posts: 139

Re: Questions about singularity version of salome_meca 2021

How to connect with container via ssh ?
Is it possible in visual studio ?

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#37 2021-10-20 16:47:44

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello,

with an ssh-server and X-server running on a server without graphics card, I just login to this server with 'ssh -X user@xxx.yyy.zzz.aaa' and launch the container there (X11 forwarding must be configured in ssh.conf [?] not sure where exactly at the moment). The GUI is then forwarded to your client. It is a bit sluggish without a graphics card but it works. It also depends a little on your connection (latency).

About visual studio, I do not know.

Mario.

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#38 2021-11-25 11:13:46

jonas loenartz
Member
Registered: 2021-10-01
Posts: 54

Re: Questions about singularity version of salome_meca 2021

Hello Mario,

First of all, I wanted to thank you and Ing.nicola for this amazing feat! Your tutorial is very concise, and I was able to install and use the MPI version of SM2021 without any issues so far. It works both, on my local machine as well as on a remote server without a GPU.
I had to run the container with the option  '--soft'  to enable software-rendering, when using it on a remote server, though. Without this option, the application crashed, when opening modules with 3D-rendering control like Paravis or AsterStudy. It did not work automatically for me, so if someone runs into this issue, start the container by using:

./salome_meca-lgpl-2021.0.0-0-20210601-scibian-9 --soft

Greetings,
Jonas

Last edited by jonas loenartz (2021-11-25 14:12:02)

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#39 2022-03-01 19:22:33

Yves POUSSET
Member
Registered: 2012-03-20
Posts: 9

Re: Questions about singularity version of salome_meca 2021

Thanks To Ing.nicola and mf for the MPI tutorial.
It worked on my debian station !

I encountered the following minor difficulties :
   - applying tutorial on new salome sif version (20211014)  does not work on my debian OS.
     Ok with 20210601 version as specified.
   - need to change access rights on /tmp/astk folder inside container  (chmod 777...
   - some tutorial commands need su, others sudo...

I finally obtained a working MPI solver.

However, until now I have a strange (normal ?) behavior:
each command is printed 4 times in log file if i use 4 mpi processors, when asrun is launched from shell (Python).

Additionnal issue : My finite element model is huge. Computation fails (lack of space in container tmp folder).
Is it a good idea - and possible - to try to increase free space inside container ?

Yves POUSSET

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#40 2022-03-28 10:25:33

VonPire
Member
Registered: 2021-01-14
Posts: 33

Re: Questions about singularity version of salome_meca 2021

Hello,

Great work from Ing. nicola and mf with this mpi+petsc version container.

I want to say that I'm a simulation engineer, not software engineer, so I really need tips with these questions:

Do you guys know how to use Intel compilers and Intel MKL mathlib with this singularity version ?

What is and where is the configuration file similar to setup.cfg (in aster-full-src-14.6.0) ?

Is it even possible to compile/build aster,mumps,petsc etc. with Intel compilers and Intel MKL with this Salome-meca singularity version ?

Best regards,
VonPire

Last edited by VonPire (2022-03-28 10:36:30)

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#41 2022-03-28 12:30:58

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello,

short answer: no. For me personally, the task of compiling such a huge software package, even with standard compilers is completely unsolvable without someone giving me instructions. It is like a foreign language, that I am unable to speak. It would take weeks for me to understand what is going on :-) . Is it worth the pain for a gain of a few % less computing time? That you'll have to decide for yourself.

Mario.

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#42 2022-03-28 12:57:18

VonPire
Member
Registered: 2021-01-14
Posts: 33

Re: Questions about singularity version of salome_meca 2021

Hello Mario,

Thank you for your reply.

I gained 30% performance gain (compared to default GNU compilers and mathlib) with "onecore/sequential" version of aster-full-src-14.6.0 with my new workstation when I compiled it with Intel compilers and Intel MKL. I guess that the performance gain would be bigger when using parallel OpenMP and MPI version that has been compiled with Intel compilers and Intel MKL. So I think that there is good motivation to investigate and try this to get working.

Best regards,
VonPire

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#43 2022-03-29 13:44:28

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello,

this seems very high to me. May I ask, is your CPU pre-Skylake (there were a lot of changes in this architecture..) or is it newer?

I am asking because newer CPUs (Sklyakeish-Xeons with lower frequency) are not always quicker in certain problems (for example thermal only simulations) compared to Ivy Lake Xeons.

Mario.

Last edited by mf (2022-03-29 13:47:15)

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#44 2022-03-29 13:54:49

VonPire
Member
Registered: 2021-01-14
Posts: 33

Re: Questions about singularity version of salome_meca 2021

Hello Mario,

My cpu is the new AMD EPYC 7443, 24-core, Octa memory channel, 4Ghz, 128 Mb L3 cache, etc.

AMD offers also own EPYC ZEN3/Milan optimized AOCC compilers (clang, clang++, flang) and AOCL mathlibrary (there are BLIS, ScaLAPACK, LibFLAME, FFTW, LibM, AOCL Sparse, AOCL enabled MUMPS), but I haven't managed to get aster working with these not even aster sequential version.

Best regards,
VonPire

Last edited by VonPire (2022-03-29 13:55:58)

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#45 2022-03-29 14:00:48

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello,

you are using Intel Compilers for AMD? What? That's blasphemy :-)

Ah that's a quite new CPU, maybe the generic compilers are not up-to-date for these newer Milans (caching is quite different in these multi-die CPUs, so I heard). I assume the Intel Compilers are updated regularly, maybe even before new CPUs arrive at customers. It could well be that the generic compilers need some flags for these CPUs, but I am only guessing here,

Mario.

Last edited by mf (2022-03-29 14:07:23)

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#46 2022-03-29 14:12:54

VonPire
Member
Registered: 2021-01-14
Posts: 33

Re: Questions about singularity version of salome_meca 2021

Hello,

Yep, it would be nice to test code_aster with AMD's own optimized compilers and mathlibs and see the difference to GNU and Intel. However AMD provides own EPYC specific compiler options for using AOCC, GNU and Intel compilers and Intel seems to work with sequential version of aster-full-src 14.6.

I could give the GNU a chance with different optimization flags. I have tried only with default flags.

I haven't managed to get working yet the openMP and MPI version of aster-full-src 14.6.

Best regards,
VonPire

Last edited by VonPire (2022-03-29 14:16:38)

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#47 2022-03-29 14:17:19

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello again,

that is great. Are these Intel Compilers still free to use, or do you have to pay for them? I remember, they were free a few years ago.

I tried the new Container with 'our' recipe for the MPI version, but I did not succeed (MUMPS did not compile and something else, I can't remember). Somebody with more understanding of this whole thing must try this :-),

Mario.

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#48 2022-03-29 14:33:30

VonPire
Member
Registered: 2021-01-14
Posts: 33

Re: Questions about singularity version of salome_meca 2021

Hello,

I'm using Intel OneAPI Base and HPC toolkit. They are free. It says: "All Intel® oneAPI Toolkits products are available at no cost." Here is the source: htt ps://www.intel.com/content/www/us/en/developer/articles/news/free-intel-software-developer-tools.html (remove the space from start)

I agree with you Mario. This would be a lot easier or quicker if there would be somebody helping with more software engineering background.

Best regards,
VonPire

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#49 2022-03-29 18:28:31

VonPire
Member
Registered: 2021-01-14
Posts: 33

Re: Questions about singularity version of salome_meca 2021

Hello Mario,

Codeaster src 16.1.8 version (seems to be latest?) (htt ps://sourceforge.net/p/codeaster/src/ci/16.1.8/tree/) from Sourceforge works with the newest salome_meca 2021.0.0-2-20211014 container with yours and ing. nicola's MPI version recipe. Just update the container and version names when using commands and update also the pkginfo.py. smile

If I understood correctly that older versions of Codeaster src doesn't work because this new container salome_meca 2021.0.0-2-20211014 have newer version of MUMPS.

Best regards,
VonPire

Last edited by VonPire (2022-03-29 18:28:58)

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#50 2022-03-29 18:43:07

mf
Member
Registered: 2019-06-18
Posts: 348

Re: Questions about singularity version of salome_meca 2021

Hello again,

oh, thank you. That's great news. Although I must say, I prefer the stable versions . But I am sure, somebody will benefit from that.

Bye,

Mario.

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