[gmx-users] Gromacs 2018.5 with CUDA
pbuscemi at q.com
pbuscemi at q.com
Wed Jan 30 17:14:12 CET 2019
Vlad,
390 is an 'old' driver now. Try something simple like installing CUDA 410.x see if that resolves the issue. if you need to update the compiler, g++ -7 may not work, but g++ -6 does.
Do NOT install the video driver from the CUDA toolkit however. If necessary, do that separately from the PPA repository.
Paul
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Benson Muite
Sent: Wednesday, January 30, 2019 10:05 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Gromacs 2018.5 with CUDA
Hi,
Do you get the same build errors with Gromacs 2019?
What operating system are you using?
What GPU do you have?
Do you have a newer version of version of GCC?
Benson
On 1/30/19 5:56 PM, Владимир Богданов wrote:
HI,
Yes, I think, because it seems to be working with nam-cuda right now:
Wed Jan 30 10:39:34 2019
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 390.77 Driver Version: 390.77 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 TITAN Xp Off | 00000000:65:00.0 On | N/A |
| 53% 83C P2 175W / 250W | 2411MiB / 12194MiB | 47% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 1258 G /usr/lib/xorg/Xorg 40MiB |
| 0 1378 G /usr/bin/gnome-shell 15MiB |
| 0 7315 G /usr/lib/xorg/Xorg 403MiB |
| 0 7416 G /usr/bin/gnome-shell 284MiB |
| 0 12510 C ..._2.11_Linux-x86_64-multicore-CUDA/namd2 235MiB |
| 0 12651 C ..._2.11_Linux-x86_64-multicore-CUDA/namd2 235MiB |
| 0 12696 C ..._2.11_Linux-x86_64-multicore-CUDA/namd2 235MiB |
| 0 12737 C ..._2.11_Linux-x86_64-multicore-CUDA/namd2 235MiB |
| 0 12810 C ..._2.11_Linux-x86_64-multicore-CUDA/namd2 235MiB |
| 0 12868 C ..._2.11_Linux-x86_64-multicore-CUDA/namd2 235MiB |
| 0 20688 C ..._2.11_Linux-x86_64-multicore-CUDA/namd2 251MiB |
+-----------------------------------------------------------------------------+
After unsuccesful gromacs run, I ran namd
Best,
Vlad
30.01.2019, 10:59, "Mark Abraham" <mark.j.abraham at gmail.com><mailto:mark.j.abraham at gmail.com>:
Hi,
Does nvidia-smi report that your GPUs are available to use?
Mark
On Wed, 30 Jan 2019 at 07:37 Владимир Богданов <bogdanov-vladimir at yandex.ru<mailto:bogdanov-vladimir at yandex.ru>>
wrote:
Hey everyone!
I need help, please. When I try to run MD with GPU I get the next error:
Command line:
gmx_mpi mdrun -deffnm md -nb auto
Back Off! I just backed up md.log to ./#md <https://vk.com/im?sel=15907114&st=%23md>.log.4#
NOTE: Detection of GPUs failed. The API reported:
GROMACS cannot run tasks on a GPU.
Reading file md.tpr, VERSION 2018.2 (single precision)
Changing nstlist from 20 to 80, rlist from 1.224 to 1.32
Using 1 MPI process
Using 16 OpenMP threads
Back Off! I just backed up md.xtc to ./#md <https://vk.com/im?sel=15907114&st=%23md>.xtc.2#
Back Off! I just backed up md.trr to ./#md <https://vk.com/im?sel=15907114&st=%23md>.trr.2#
Back Off! I just backed up md.edr to ./#md <https://vk.com/im?sel=15907114&st=%23md>.edr.2#
starting mdrun 'Protein in water'
30000000 steps, 60000.0 ps.
I built gromacs with MPI=on and CUDA=on and the compilation process looked good. I ran gromacs 2018.2 with CUDA 5 months ago and it worked, but now it doesn't work.
Information from *.log file:
GROMACS version: 2018.2
Precision: single
Memory model: 64 bit
MPI library: MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: CUDA
SIMD instructions: AVX_512
FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Built on: 2018-06-24 02:55:16
Built by: vlad at vlad [CMAKE]
Build OS/arch: Linux 4.13.0-45-generic x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Core(TM) i7-7820X CPU @ 3.60GHz
Build CPU family: 6 Model: 85 Stepping: 4
Build CPU features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2
ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 5.4.0
C compiler flags: -mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 5.4.0
C++ compiler flags: -mavx512f -mfma -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
CUDA compiler: /usr/local/cuda-9.2/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Wed_Apr_11_23:16:29_CDT_2018;Cuda compilation tools, release 9.2, V9.2.88
CUDA compiler
flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;-D_FORCE_INLINES;;
;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver: 9.10
CUDA runtime: 32.64
NOTE: Detection of GPUs failed. The API reported:
GROMACS cannot run tasks on a GPU.
Any idea what I am doing wrong?
Best,
Vlad
--
C уважением, Владимир А. Богданов
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