On 5/21/13 5:41 AM, Vishal Kumar Jaiswal wrote:
Following your advice I compiled gromacs with DGMX_CPU_ACCELERATION=SSE4.1
and now it is working :) . Thanks a lot
I suggested this as a diagnostic measure (not a fix), and it is good that it is
working properly, but is also indicative of a problem with the AVX_256
acceleration. Please file a bug report on redmine.gromacs.org with all the
details provided below, as well as .log files from successful and failed runs,
and a .tpr file that can be used to reproduce the problem. With that
information, we should be able to fix the bug so no one else encounters it again.
-Justin
On Tue, May 21, 2013 at 7:45 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 5/20/13 9:00 AM, Vishal Kumar Jaiswal wrote:
LAPTOP- WORKING
PC -NOT WORKING
Gromacs version: VERSION 4.6.1
VERSION 4.6.1
Precision: single
same
Memory model: 32 bit
64 bit
MPI library: thread_mpi
same
OpenMP support: enabled
same
GPU support: enabled
disabled
invsqrt routine: gmx_software_invsqrt(x)
same
CPU acceleration: SSE4.1
AVX_256
FFT library: fftw-3.2.2
fftw-3.3.3-sse2
Large file support: enabled
same
RDTSCP usage: disabled
enabled
Built on: Fri Mar 15 14:30:08 IST 2013
Fri May 10 13:45:48 IST 2013
Built by: vishal@vishal-VPCCW16FG [CMAKE]
vishal@aditya-HCL-Desktop [CMAKE]
Build OS/arch: Linux 3.0.0-12-generic i686
Linux 3.0.0-19-generic x86_64
Build CPU vendor: GenuineIntel
GenuineIntel
Build CPU brand: Intel(R) Core(TM)2 Duo CPU P8700 @ 2.53GHz
Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
Build CPU family: 6 Model: 23 Stepping: 10
6 Model: 42 Stepping: 7
Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2
sse3 sse4.1 ssse3
: PC - aes apic avx clfsh cmov cx8 cx16 htt
lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3
sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/gcc GNU gcc (Ubuntu/Linaro 4.6.1-9ubuntu3)
4.6.1
PC - /usr/bin/gcc GNU gcc (Ubuntu/Linaro
4.6.1-9ubuntu3) 4.6.1
C compiler flags: -msse4.1 -Wextra -Wno-missing-field-**initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
PC - -mavx -Wextra
-Wno-missing-field-**initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU c++ (Ubuntu/Linaro 4.6.1-9ubuntu3)
4.6.1
PC - none
C++ compiler flags: -msse4.1 -Wextra -Wno-missing-field-**initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
PC -none
CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c)
2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:24:42_PDT_2012;**Cuda
compilation tools, release 5.0, V0.2.1221
PC (none)
CUDA driver: 5.0 none
CUDA runtime: 5.0 none
These are taken from gromacs log files. ( Though i have CUDA installed on
laptop i dont use it for GROMACS as the NVIDIA compte capability is 1.2)
I am able to run the tutorial on PC now using GROMACS 4.5.7
Please tell me if you want more details.
It would be useful to get to the root of the error, because this smells of
a bug. One idea that comes to mind is to manually set SSE4.1 as the CPU
acceleration on the non-working PC to see if AVX_256 is the problem.
-Justin
On Mon, May 20, 2013 at 5:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 5/20/13 2:29 AM, Vishal Kumar Jaiswal wrote:
I am trying to complete the lysozyme in water tutorial in gromacs 4.6.1
and
i am getting this error in the energy minimization step
I was able to complete the entire tutorial on another computer ( my
personal laptop) . ( I was getting the same error while doing energy
minimization on another system (polymer in water) which forced me to
check
gromacs correcctness by doing the lysozyme tutorial)
How do the configurations of your laptop and the problematic machine
differ?
-Justin
The following is the verbose output to my terminal :
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= -nan Fmax= 1.50489e+13,
atom=
14918
------------------------------****-------------------------
Program mdrun, VERSION 4.6.1
Source code file: /home/vishal/Downloads/****
gromacs-4.6.1/src/mdlib/pme.c,
line: 827
Fatal error:
3483 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
Following is the entry from "em.log" file
Linking all bonded interactions to atoms
There are 8522 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1
The initial domain decomposition cell size is: X 1.83 nm
The maximum allowed distance for charge groups involved in interactions
is:
non-bonded interactions 1.000 nm
two-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
Making 1D domain decomposition grid 4 x 1 x 1, home cell index 0 0 0
Initiating Steepest Descents
Charge group distribution at step 0: 3184 3300 3308 3255
Grid: 5 x 11 x 11 cells
Started Steepest Descents on node 0 Mon May 20 11:36:21 2013
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step Time Lambda
0 0.00000 0.00000
DD step 0 load imb.: force 8.8%
------------------------------****-------------------------
Program mdrun, VERSION 4.6.1
Source code file: /home/vishal/Downloads/****
gromacs-4.6.1/src/mdlib/pme.c,
line: 827
Fatal error:
3483 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
The following is the hardware information of the pc on which error is
showing ttaken from "em.log" file
Gromacs version: VERSION 4.6.1
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.3-sse2
Large file support: enabled
RDTSCP usage: enabled
Built on: Fri May 10 13:45:48 IST 2013
Built by: vishal@aditya-HCL-Desktop [CMAKE]
Build OS/arch: Linux 3.0.0-19-generic x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
Build CPU family: 6 Model: 42 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
ssse3 tdt x2apic
C compiler: /usr/bin/gcc GNU gcc (Ubuntu/Linaro 4.6.1-9ubuntu3)
4.6.1
C compiler flags: -mavx -Wextra -Wno-missing-field-****initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value
-fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
--
==============================****==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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