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.
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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
> posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read
> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
