Hi All,
Thought I need to bring this up again...I encountered large CUDA test error with DPFP precision mode. The maximum relative errors are usually at the level of e-01.
Below I attached .diff and .log from test_amber_cuda and test_at_cuda, respectively.
https://drive.google.com/drive/folders/1wAUz_8538PwKDSVbM1ZR4wuDQsuybbKG?usp=sharing
And the forwarded info are my hardware sys and how I install the AMBER20.
Since I'm really in a hurry in running a few MD jobs. Would anyone have an idea if I could run classical MD with SPFP mode (which is the default) safely? Thank you!
Best,
Guqin
===============================================================================================================
Hi David,
Thanks for the reply. I supplemented my system in another reply and it probably drowned in the messages.
Here is my system:
CentOS 7, 32 Xeon Gold cpus .3.3GHz, 1 Quadro RTX 5000 CUDA toolkit is 11.1
I followed the instructions on manual.
According to
https://ambermd.org/pmwiki/index.php/Main/CMake-Quick-Start. Cmake3 is recommended for CentOS 7. So I installed cmake3 and use cmake3 instead of cmake. For eg, in run_make script, cmake is changed to cmake3. In my system, a symbolic link of cmake is created directing to cmake3 in /usr/bin.
I installed devtoolset-8 to make sure all gnu compilers are version with 8.3.1.
I downloaded mpich3.3.2 package for parallel installation.
These are all the changes I've made for AMBER20 serial installation. For parallel and GPU installation, nothing changed except for turning -DMPI and -DCUDA flag to TRUE, respectively.
I hope these could help. Please let me know what else you need for troubleshoot The differences are quite large in GPU DPFP tests...I'm not sure if I can run any MD now...with default SPFP...?
Thanks a lot for the help!
-Guqin
=================================================================================================================
-----邮件原件-----
发件人: David A Case [mailto:david.case.rutgers.edu]
发送时间: 2021年4月24日 21:32
收件人: AMBER Mailing List <amber.ambermd.org>
主题: [ambermd.org代发]Re: [AMBER] Max relative errors questions in parallel and cuda.serial test
On Thu, Apr 22, 2021, 石谷沁 wrote:
>I double-checked the cuda.serial log. The possible failures all came out at DPFP:
>==============================================================
>cd myoglobin/ && ./Run_md_myoglobin_igb7 DPFP yes
>Note: The following floating-point exceptions are signalling:
>IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing
>myoglobin_md_igb7.out.GPU_DPFP with myoglobin_md_igb7.out possible
>FAILURE: check myoglobin_md_igb7.out.dif
This is concerning.
>
>According to manual, SPFP is the default precision model for
>pmemd.cuda. And I didn’t get any failures report on SPFP. So I guess I
>can ignore those errors with DPFP in most general situations?
Again, very odd: the expectation is that DPFP tests will all pass, when compared to a CPU output, but that a fair number of SPFP tests will fail with roundoff errors.
So, I think you have genuine problems. Can you say (again?) what GPU you have, and what CUDA SDK version? Maybe the GPU gurus on the list (I am not one of them) will spot something.
Also, please say what changes you made to run_cmake (if you used that), and what command(s) you used to run the tests.
....dac
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Received on Tue Apr 27 2021 - 18:00:03 PDT
