Re: [gmx-users] Question on installation
May be just let gromacs build its own fftw3 library, by using -DGMX_BUILD_OWN_FFTW=ON in the cmake command, is a better idea? On Mon, Dec 8, 2014 at 2:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/8/14 12:38 PM, Igor Shchechkin wrote: Dear Gromacs users, I have obtained the error Cannot find fftw3f library installing 4.5.3 version of Gromacs. fftw 3.3.4 version has been preliminary installed, names of include and lib directories present in CPPFLAGS and LDFLAGS configuring Gromacs, both FFTW and Gromacs are configured in single precision. Mailing list is sought and the information found is irrelevant to my case. Could you, please, help me? You need to provide the actual command(s) you issued. If FFTW is installed, whatever you specified as a path during Gromacs installation was probably just wrong. -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.
[gmx-users] Question on installation
Dear Gromacs users, I have obtained the error Cannot find fftw3f library installing 4.5.3 version of Gromacs. fftw 3.3.4 version has been preliminary installed, names of include and lib directories present in CPPFLAGS and LDFLAGS configuring Gromacs, both FFTW and Gromacs are configured in single precision. Mailing list is sought and the information found is irrelevant to my case. Could you, please, help me? Best regards, Igor Shchechkin -- 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] Question on installation
On 12/8/14 12:38 PM, Igor Shchechkin wrote: Dear Gromacs users, I have obtained the error Cannot find fftw3f library installing 4.5.3 version of Gromacs. fftw 3.3.4 version has been preliminary installed, names of include and lib directories present in CPPFLAGS and LDFLAGS configuring Gromacs, both FFTW and Gromacs are configured in single precision. Mailing list is sought and the information found is irrelevant to my case. Could you, please, help me? You need to provide the actual command(s) you issued. If FFTW is installed, whatever you specified as a path during Gromacs installation was probably just wrong. -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.
[gmx-users] question about installation of gmx on Cray linux
Dear Gromacs Developers and Experts: I noticed that the performance of gromacs on Cray linux clusters is only 36.7% of the normal. The following is the detail about the installation -- CC=gcc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/opt/cray/modulefiles/cray-mpich/6.3.0 cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DGMX_MPI=ON -DBUILD_SHARED_LIBS=off -DCMAKE_SKIP_RPATH=ON -DCMAKE_INSTALL_PREFIX=~/App/GROMACS make F77=gfortran make install -- This is the bash_profile: - module swap PrgEnv-pgi PrgEnv-gnu module load cmake export PATH=/home/test/App/GROMACS/bin:$PATH - Is there any suggestion for my installation to improve the efficiency? Thanks! Thomas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] question about installation of gmx on Cray linux
Yes. Please start by reading the reply Justin made a few days ago. Your normal is unknown to us. Mark On Jun 24, 2014 10:29 PM, Tom dna...@gmail.com wrote: Dear Gromacs Developers and Experts: I noticed that the performance of gromacs on Cray linux clusters is only 36.7% of the normal. The following is the detail about the installation -- CC=gcc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/opt/cray/modulefiles/cray-mpich/6.3.0 cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DGMX_MPI=ON -DBUILD_SHARED_LIBS=off -DCMAKE_SKIP_RPATH=ON -DCMAKE_INSTALL_PREFIX=~/App/GROMACS make F77=gfortran make install -- This is the bash_profile: - module swap PrgEnv-pgi PrgEnv-gnu module load cmake export PATH=/home/test/App/GROMACS/bin:$PATH - Is there any suggestion for my installation to improve the efficiency? Thanks! Thomas -- 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.
