[gmx-users] how to generate executable file g_energy_mpi ?
Hi everyone. I am new to Gromacs and have some question in the building part. I can only genarate mdrun_mpi when set the DGMX_BUILD_MDRUN_ONLY to ON and when I set it to OFF, it can only produce gmx_mpi and template in the bin directory. What is the different between mdrun_mpi and gmx_mpi ? Another question, I want to produce .xvg file to do some analysis and have to use g_energy_mpi to read the .edr file, so how can I generate g_energy_mpi ? Thanks:) Vincent -- 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.
Re: [gmx-users] how to generate executable file g_energy_mpi ?
On 10/23/14 6:37 AM, Vinson Leung wrote: Hi everyone. I am new to Gromacs and have some question in the building part. I can only genarate mdrun_mpi when set the DGMX_BUILD_MDRUN_ONLY to ON and when I set it to OFF, it can only produce gmx_mpi and template in the bin directory. What is the different between mdrun_mpi and gmx_mpi ? Another question, I want to produce .xvg file to do some analysis and have to use g_energy_mpi to read the .edr file, so how can I generate g_energy_mpi ? Thanks:) The only program that benefits from MPI is mdrun. None of the analysis tools are parallelized via MPI. -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.
Re: [gmx-users] how to generate executable file g_energy_mpi ?
and how can I get those analysis tools? On Thu, Oct 23, 2014 at 7:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/23/14 6:37 AM, Vinson Leung wrote: Hi everyone. I am new to Gromacs and have some question in the building part. I can only genarate mdrun_mpi when set the DGMX_BUILD_MDRUN_ONLY to ON and when I set it to OFF, it can only produce gmx_mpi and template in the bin directory. What is the different between mdrun_mpi and gmx_mpi ? Another question, I want to produce .xvg file to do some analysis and have to use g_energy_mpi to read the .edr file, so how can I generate g_energy_mpi ? Thanks:) The only program that benefits from MPI is mdrun. None of the analysis tools are parallelized via MPI. -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. -- 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.
Re: [gmx-users] how to generate executable file g_energy_mpi ?
On 10/23/14 7:48 AM, Vinson Leung wrote: and how can I get those analysis tools? http://www.gromacs.org/Documentation/Installation_Instructions Everything gets built by default unless you use -DGMX_BUILD_MDRUN_ONLY=ON -Justin On Thu, Oct 23, 2014 at 7:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/23/14 6:37 AM, Vinson Leung wrote: Hi everyone. I am new to Gromacs and have some question in the building part. I can only genarate mdrun_mpi when set the DGMX_BUILD_MDRUN_ONLY to ON and when I set it to OFF, it can only produce gmx_mpi and template in the bin directory. What is the different between mdrun_mpi and gmx_mpi ? Another question, I want to produce .xvg file to do some analysis and have to use g_energy_mpi to read the .edr file, so how can I generate g_energy_mpi ? Thanks:) The only program that benefits from MPI is mdrun. None of the analysis tools are parallelized via MPI. -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. -- == 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.
Re: [gmx-users] how to generate executable file g_energy_mpi ?
On 10/23/14 8:03 AM, Vinson Leung wrote:
But I remove the option -DGMX_BUILD_MDRUN_ONLY=ON and can only get
gmx_mpi and template. There is no those analysis tools and my Gromacs
version is 5.0.2.
My build congfiure is like below:
=
export CCDIR=/opt/intel/composer_xe_2013_sp1.2.144/bin/intel64
export CMAKE_PREFIX_PATH=/opt/mpich
export ZLIB_DIR=/usr
../../cmake-3.0.2/bin/cmake .. \
-DBUILD_SHARED_LIBS=OFF \
-DGMX_PREFER_STATIC_LIBS=ON \
-DGMX_FFT_LIBRARY=mkl \
-DCMAKE_INSTALL_PREFIX=/home/vincent/gromacs-5.0.2/build-all \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_XML=OFF \
-DGMX_SOFTWARE_INVSQRT=OFF \
-DGMX_SKIP_DEFAULT_CFLAGS=ON \
-DCMAKE_EXE_LINKER_FLAGS=-L${ZLIB_DIR}/lib64 -mkl=sequential \
-DCMAKE_CXX_COMPILER=icpc \
-DCMAKE_C_COMPILER=icc \
-DCMAKE_C_FLAGS= -xAVX -O3 -vec-report1 -fno-alias -g -DNDEBUG -ip
-funroll-all-loops -fimf-domain-exclusion=15 -I${ZLIB_DIR}/include \
-DCMAKE_CXX_FLAGS= -xAVX -O3 -vec-report1 -fno-alias -g -DNDEBUG -ip
-funroll-all-loops -fimf-domain-exclusion=15 -I${ZLIB_DIR}/include
==
Is there anything I miss?
In version 5.0, every Gromacs program is now a module of the gmx binary, so
g_energy is just a symlink to gmx energy, which is now the actual command.
There is no point in compiling anything other than mdrun with MPI support, so
set -DGMX_MPI=OFF unless doing an mdrun-only build.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
--
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* Please search the archive at
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Re: [gmx-users] how to generate executable file g_energy_mpi ?
Thanks. It seem to much more clear for me:).
I have compiled again with -DGMX_MPI=OFF. Now I have only two executable
file (gmx and template) in the bin dir. If I want to generate .xvg file
and I already have .edr file. What is the comand line exactly ?
Vincent
On Thu, Oct 23, 2014 at 8:05 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/23/14 8:03 AM, Vinson Leung wrote:
But I remove the option -DGMX_BUILD_MDRUN_ONLY=ON and can only get
gmx_mpi and template. There is no those analysis tools and my Gromacs
version is 5.0.2.
My build congfiure is like below:
=
export CCDIR=/opt/intel/composer_xe_2013_sp1.2.144/bin/intel64
export CMAKE_PREFIX_PATH=/opt/mpich
export ZLIB_DIR=/usr
../../cmake-3.0.2/bin/cmake .. \
-DBUILD_SHARED_LIBS=OFF \
-DGMX_PREFER_STATIC_LIBS=ON \
-DGMX_FFT_LIBRARY=mkl \
-DCMAKE_INSTALL_PREFIX=/home/vincent/gromacs-5.0.2/build-all \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_XML=OFF \
-DGMX_SOFTWARE_INVSQRT=OFF \
-DGMX_SKIP_DEFAULT_CFLAGS=ON \
-DCMAKE_EXE_LINKER_FLAGS=-L${ZLIB_DIR}/lib64 -mkl=sequential \
-DCMAKE_CXX_COMPILER=icpc \
-DCMAKE_C_COMPILER=icc \
-DCMAKE_C_FLAGS= -xAVX -O3 -vec-report1 -fno-alias -g -DNDEBUG -ip
-funroll-all-loops -fimf-domain-exclusion=15 -I${ZLIB_DIR}/include \
-DCMAKE_CXX_FLAGS= -xAVX -O3 -vec-report1 -fno-alias -g -DNDEBUG -ip
-funroll-all-loops -fimf-domain-exclusion=15 -I${ZLIB_DIR}/include
==
Is there anything I miss?
In version 5.0, every Gromacs program is now a module of the gmx binary,
so g_energy is just a symlink to gmx energy, which is now the actual
command. There is no point in compiling anything other than mdrun with MPI
support, so set -DGMX_MPI=OFF unless doing an mdrun-only build.
-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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* 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
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mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to generate executable file g_energy_mpi ?
On 10/23/14 8:26 AM, Vinson Leung wrote: Thanks. It seem to much more clear for me:). I have compiled again with -DGMX_MPI=OFF. Now I have only two executable file (gmx and template) in the bin dir. If I want to generate .xvg file and I already have .edr file. What is the comand line exactly ? gmx energy -f *.edr Note that you can get the help information (syntax, required input, etc) for any program with gmx help [program] Everything is also in the printed manual and simple tasks are well covered in most tutorials available online. -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.
Re: [gmx-users] how to generate executable file g_energy_mpi ?
Thank you very much:) It help me a lot ! Best Vincent On Thu, Oct 23, 2014 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/23/14 8:26 AM, Vinson Leung wrote: Thanks. It seem to much more clear for me:). I have compiled again with -DGMX_MPI=OFF. Now I have only two executable file (gmx and template) in the bin dir. If I want to generate .xvg file and I already have .edr file. What is the comand line exactly ? gmx energy -f *.edr Note that you can get the help information (syntax, required input, etc) for any program with gmx help [program] Everything is also in the printed manual and simple tasks are well covered in most tutorials available online. -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. -- 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.
