Drivers & Software

[pimooni]

Dear Community,

This is Pim, a new EPYC user. I just DIYed a workstation as following:

    - Supermicro H11DSi

    - EPYC 7B12 * 2

    - Samsung RECC 3200 32G * 16

    -  Samsung 980 Pro 2t

    - Centos 7 installed

I'm trying to compile and install gromacs from .tar.gz. I referred to following official document and prepared AOCC 4.0 & AOCL 4.0 environments, accordingly (by downloading and installing .rpm from AMD site).

https://www.amd.com/system/files/documents/EPYC-7002-Gromacs-Molecular-Dynamics-Simulation.pdf

However, when I tried to compile with clang/clang++, the configure can be down while  all the make check items were failed (saying SEGFAULT):

    $ cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/opt/AMD/aocl/aocl-linux-aocc-4.0/lib_LP64/libfftw3f.so -DFFTWF_INCLUDE_DIR=/opt/AMD/aocl/aocl-linux-aocc-4.0/include_LP64/

    $ make -j200

    $ make check -j200

Would someone help on this?

Great appreciations in advance.

Pim

[pimooni]

Hi team,

Very recently, I DIYed a workstation with following hardware:
- Supermicro H11DSi
- EPYC 7B12 * 2 (128C 256T)
- Samsung RECC 3200 32G * 16 = 512G
- Samsung 980 Pro 2t

On such machine, I prepared following environments:
- Centos 7 with kernel ver. 6.2.8-1.el7.elrepo.x86_64
- GLIBC updated to 2.28
- GCC & G++ 11 installed via command “$yum install devtoolset-11-gcc*” and source xxx/enable
- make 4.3 & cmake 3.25.3
- AOCC 4.0 & AOCL 4.0 installed

I downloaded GROMACS 2023 .tar.gz from official site and made installation according to guidance.

— Trial I —
I first compiled gmx with gcc/g++:
$ cmake … -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2023-gcc
-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
-DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=ON

Everything is smooth and I started running a system [3500 water + 256 met + 128 eth] for a purpose of detecting molecular behaviors in interface.
However, the simulation got freezed / hanging / stuck at approx. 10 million steps. No any more steps were added (just stuck there like being frozen) and the info on screen no longer changed. I input ctrl+c and it showed core dumped. While I checked the log file, there’s no additional information except normal simulation step data.

I repeated and got into same situation. The only difference was that the simulation got stuck in different steps - it seems to be random or something else.

— Trial II —
I searched on google and found some traces. However NO clear solution was given. I then re-installed gromacs according to AMD official benchmark page:
https://www.amd.com/system/files/documents/EPYC-7002-Gromacs-Molecular-Dynamics-Simulation.pdf 2

It was mentioned that their gmx was compiled with AOCC 2.0, AOCL 2.0 and Open MPI 4.0.0 - I didn’t turn on DGMX_MPI in my workstation since it’s just single node.
I then compiled in such way:
$ cmake … -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2023-aocc
-DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
-DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/PATH/TO/FFTW3
-DGMX_OPENMP=ON

The installation itself seems to be smooth (AGAIN) and the simulation got freezed / hanging / stuck (AGAIN). I repeated the simulation and was led to same dilemma.

Please see beneath attached screenshot for a straightforward view.

— QUESTION ----

Is this related to my EPYC 7B12 cpu?
Or, is this related to my gmx installation (like, I missed some key FLAG for AMD EPYC cpu compilation)?
Anyway, I think this may not be an ONLY case in community.
Please kindly help.
Any suggestion, comment, hint would be more than welcome.
Please save my new workstation and my research from this morass situation : (

Regards
Pim