Hi Mark,
Nothing has been installed yet, so the commands were issued from
/build/bin and so I am not sure about the output of that mdrun-test (let
me know what exact command could make it more informative).
Thank you,
Alex
***
> ./gmx -version
GROMACS version: 2018
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: CUDA
SIMD instructions: AVX2_256
FFT library: fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-1.11.0
Tracing support: disabled
Built on: 2018-02-06 19:30:36
Built by: smolyan@647trc-md1 [CMAKE]
Build OS/arch: Linux 4.4.0-112-generic x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Xeon(R) CPU E5-2699 v4 @ 2.20GHz
Build CPU family: 6 Model: 79 Stepping: 1
Build CPU features: aes apic avx avx2 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: -march=core-avx2 -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 5.4.0
C++ compiler flags: -march=core-avx2 -std=c++11 -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda
compiler driver;Copyright (c) 2005-2017 NVIDIA Corporation;Built on
Fri_Nov__3_21:07:56_CDT_2017;Cuda compilation tools, release 9.1, V9.1.85
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;;
;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver: 9.10
CUDA runtime: 9.10
> ldd -r ./mdrun-test
linux-vdso.so.1 => (0x00007ffcfcc3e000)
libgromacs.so.3 =>
/home/smolyan/scratch/gmx2018_install_temp/gromacs-2018/build/bin/./../lib/libgromacs.so.3
(0x00007faa58f8f000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007faa58d72000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007faa589f0000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007faa586e7000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007faa584d1000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007faa58107000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007faa57f03000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007faa57cfb000)
libcufft.so.9.1 => /usr/local/cuda/lib64/libcufft.so.9.1
(0x00007faa5080e000)
libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5
(0x00007faa505d4000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1
(0x00007faa503b2000)
/lib64/ld-linux-x86-64.so.2 (0x00007faa5c1ad000)
libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1
(0x00007faa501a7000)
libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7
(0x00007faa4ff9d000)
On 2/7/2018 5:13 AM, Mark Abraham wrote:
Hi,
I checked back with the CUDA-facing GROMACS developers. They've run the
code with 9.1 and believe there's no intrinsic problem within GROMACS.
So I don't have much to suggest other then rebuilding everything cleanly,
as this is an internal non-descript cuFFT/driver error that is not supposed
to happen,
especially in mdrun-test with its single input system, and it will prevent
him from using -pme gpu.
The only thing PME could do better is to show more meaningful error
messages (which would have to be hardcoded anyway as cuFFT doesn't even
have human readable strings for error codes).
If you could share the output of
* gmx -version
* ldd -r mdrun-test
then perhaps we can find an issue (or at least report to nvidia usefully).
Ensuring you are using the CUDA driver that came with the CUDA runtime is
most likely to work smoothly.
Mark
On Tue, Feb 6, 2018 at 9:24 PM Alex <nedoma...@gmail.com> wrote:
And this is with:
gcc --version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.6) 5.4.0 20160609 <020-16%2006%2009>
On Tue, Feb 6, 2018 at 1:18 PM, Alex <nedoma...@gmail.com> wrote:
Hi all,
I've just built the latest version and regression tests are running. Here
is one error:
"Program: mdrun-test, version 2018
Source file: src/gromacs/ewald/pme-3dfft.cu (line 56)
Fatal error:
cufftPlanMany R2C plan failure (error code 5)"
This is with CUDA 9.1.
Anything to worry about?
Thank you,
Alex
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