Re: [gmx-users] GPU acceleration

[יוכבד]

but still shouldn't I see some acceleration?
The other process is not using the GPUs at all only CPUs

On Mon, Jun 27, 2016 at 4:25 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 6/27/16 9:12 AM, יוכבד wrote:
>
>> here's a link to the log file
>>
>> https://drive.google.com/file/d/0By0KVsEJPLGjOU1oaGxzcjNBS28/view?usp=sharing
>>
>> The  computer is 4GPUs and 32 CPUs but some GPUs were in use hence only
>> 15-16 were used.
>>
>>
> That's not what
>
> gmx mdrun -v -deffnm nvt_New -nb gpu
>
> will do.  That command will attempt to use all resources available on the
> machine, all 32 CPU and all 4 GPU.  The .log file confirms this is the
> case.  If you're running multiple processes on the same machine, you need
> to appropriately define what should be used for each run, using -pin,
> -pinoffset, -gpu_id, -nt, -ntmpi, etc as needed, otherwise they're all
> going to try to use everything, and end up fighting each other, slowing
> everything down.
>
> -Justin
>
>
> Thanks
>>
>> On Mon, Jun 27, 2016 at 3:52 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 6/27/16 8:49 AM, יוכבד wrote:
>>>
>>> Hi
>>>> I've recently installed GROMACS 5.1.2.
>>>> I ran the benchmarks files of rnase (rnase_dodec_vsites) on my machine
>>>> using 4GPUs and 32 CPU and I got the performances of ~330ns/day
>>>>
>>>> Now I'm tring to run my system but I don't see any acceleration (a 500ps
>>>> nvt equilibration takes close to 2hr (6.7ns/day)- This was using 4 GPUs
>>>> and
>>>> 15 CPUs.
>>>>
>>>> What am I missing here?
>>>>
>>>> attached is my mdp file and the command used was
>>>>
>>>>
>>> The list does not accept attachments.  The .log files are the most
>>> informative as the end contains a full performance breakdown; if you wish
>>> to share them, upload them to a file sharing service and provide a URL.
>>>
>>> The actual performance depends largely on the content/size of the system.
>>> Perhaps you have a bottleneck due to the size of the system such that you
>>> cannot efficiently utilize all 4 GPU and 15 CPUs (an odd combination,
>>> anyway) simultaneously.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
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>>> posting!
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] GPU acceleration

[יוכבד]

here's a link to the log file
https://drive.google.com/file/d/0By0KVsEJPLGjOU1oaGxzcjNBS28/view?usp=sharing

The  computer is 4GPUs and 32 CPUs but some GPUs were in use hence only
15-16 were used.

Thanks

On Mon, Jun 27, 2016 at 3:52 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 6/27/16 8:49 AM, יוכבד wrote:
>
>> Hi
>> I've recently installed GROMACS 5.1.2.
>> I ran the benchmarks files of rnase (rnase_dodec_vsites) on my machine
>> using 4GPUs and 32 CPU and I got the performances of ~330ns/day
>>
>> Now I'm tring to run my system but I don't see any acceleration (a 500ps
>> nvt equilibration takes close to 2hr (6.7ns/day)- This was using 4 GPUs
>> and
>> 15 CPUs.
>>
>> What am I missing here?
>>
>> attached is my mdp file and the command used was
>>
>
> The list does not accept attachments.  The .log files are the most
> informative as the end contains a full performance breakdown; if you wish
> to share them, upload them to a file sharing service and provide a URL.
>
> The actual performance depends largely on the content/size of the system.
> Perhaps you have a bottleneck due to the size of the system such that you
> cannot efficiently utilize all 4 GPU and 15 CPUs (an odd combination,
> anyway) simultaneously.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] GPU acceleration

[יוכבד]

Hi
I've recently installed GROMACS 5.1.2.
I ran the benchmarks files of rnase (rnase_dodec_vsites) on my machine
using 4GPUs and 32 CPU and I got the performances of ~330ns/day

Now I'm tring to run my system but I don't see any acceleration (a 500ps
nvt equilibration takes close to 2hr (6.7ns/day)- This was using 4 GPUs and
15 CPUs.

What am I missing here?

attached is my mdp file and the command used was
 gmx mdrun -v -deffnm nvt_New -nb gpu

Thanks
Yocheved
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Re: [gmx-users] Installing GROMACS 5.1.2 om GPU

[יוכבד]

The problem is the gcc installed on our cluster is to old and it is not
possible to upgrade at the moment.

On Wed, May 25, 2016 at 1:44 PM, Mark Abraham 
wrote:

> Hi,
>
> You need to follow Intel's instructions for accessing the compiler -
> including running their magic scripts from each shell that you want to
> compile from. (Or save yourself some pain, use gcc, and probably run
> slightly faster.)
>
> Mark
>
> ‪On Wed, May 25, 2016 at 10:43 AM ‫יוכבד‬‎  wrote:‬
>
>> Hi
>>
>> I've been having lots of trouble installing gromacs on our GPU machine.
>>
>> I have Intel2015 Compilers on my machine which are identified correctly
>> during configuration.
>>
>> /private/gnss/cmake-2.8.11.2/bin/cmake ..
>> -DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2
>> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/
>> -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_FFT_LIBRARY=mkl
>> -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include
>>
>> However when I run the make I get alot of warnings and finally the
>> following error:
>>
>> /private/gnss/gromacs-5.1.2/src/external/boost/boost/config/compiler/in
>> tel.hpp(93): remark #193: zero used for undefined preprocessing identifier
>> "_WCHAR_T_DEFINED"
>> # if ((_WCHAR_T_DEFINED + 0) == 0) && ((_WCHAR_T + 0) == 0)
>> ^
>>
>> Linking CXX executable ../../bin/template
>> ld: warning: libimf.so, needed by ../../lib/libgromacs.so.1.2.0, not found
>> (try using -rpath or -rpath-link)
>> ld: warning: libsvml.so, needed by ../../lib/libgromacs.so.1.2.0, not
>> found
>> (try using -rpath or -rpath-link)
>> ld: warning: libirng.so, needed by ../../lib/libgromacs.so.1.2.0, not
>> found
>> (try using -rpath or -rpath-link)
>> ld: warning: libintlc.so.5, needed by ../../lib/libgromacs.so.1.2.0, not
>> found (try using -rpath or -rpath-link)
>> ld: ../../bin/template: hidden symbol `__intel_cpu_features_init_x' in
>>
>> /opt/intel/composer_xe_2015.5.223/compiler/lib/intel64/libirc.a(cpu_feature_disp.o)
>> is referenced by DSO
>> ld: final link failed: Nonrepresentable section on output
>> make[2]: *** [bin/template] Error 1
>> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> make: *** [all] Error 2
>>
>> all the files which are not found do exist in the compiler libraries and
>> it
>> is added to my path.
>>
>> Any suggestions how to solve this?
>>
>> Thanks
>>
>> Yocheved
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
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[gmx-users] Installing GROMACS 5.1.2 om GPU

[יוכבד]

Hi

I've been having lots of trouble installing gromacs on our GPU machine.

I have Intel2015 Compilers on my machine which are identified correctly
during configuration.

/private/gnss/cmake-2.8.11.2/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2
-DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/
-DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_FFT_LIBRARY=mkl
-DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include

However when I run the make I get alot of warnings and finally the
following error:

/private/gnss/gromacs-5.1.2/src/external/boost/boost/config/compiler/in
tel.hpp(93): remark #193: zero used for undefined preprocessing identifier
"_WCHAR_T_DEFINED"
# if ((_WCHAR_T_DEFINED + 0) == 0) && ((_WCHAR_T + 0) == 0)
^

Linking CXX executable ../../bin/template
ld: warning: libimf.so, needed by ../../lib/libgromacs.so.1.2.0, not found
(try using -rpath or -rpath-link)
ld: warning: libsvml.so, needed by ../../lib/libgromacs.so.1.2.0, not found
(try using -rpath or -rpath-link)
ld: warning: libirng.so, needed by ../../lib/libgromacs.so.1.2.0, not found
(try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../../lib/libgromacs.so.1.2.0, not
found (try using -rpath or -rpath-link)
ld: ../../bin/template: hidden symbol `__intel_cpu_features_init_x' in
/opt/intel/composer_xe_2015.5.223/compiler/lib/intel64/libirc.a(cpu_feature_disp.o)
is referenced by DSO
ld: final link failed: Nonrepresentable section on output
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

all the files which are not found do exist in the compiler libraries and it
is added to my path.

Any suggestions how to solve this?

Thanks

Yocheved
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