Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
Dear Gromacs-Users, Is there any update on this issue? I have used the following flags for version 2019.3 /apps/codes/cmake/3.15.4/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_BUILD_MDRUN_ONLY=ON and getting compilation error which says: [ 58%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o icpc: error #10105: /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom: core dumped icpc: warning #10102: unknown signal(-497903120) icpc: error #10106: Fatal error in /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom, terminated by unknown compilation aborted for /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1) make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o] Error 1 make[2]: *** Waiting for unfinished jobs make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 make: *** [all] Error 2 Your help will be highly appreciated. Thanking you. With regards, Rajib On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh wrote: > I have tried this command line: > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl > -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -DGMX_OPENMP=ON > -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2 > -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc" > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc" > -DREGRESSIONTEST_DOWNLOAD=ON > which had no errors for *cmake* or *make -j 4*, but *make check* gave me an > error: > ... > [100%] Running all tests except physical validation > Test project /home/doroshl/gromacs-2019.3/build > Start 1: TestUtilsUnitTests > 1/46 Test #1: TestUtilsUnitTests ..***Failed0.00 sec > /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while loading > shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No > such file or directory > ... > 0% tests passed, 46 tests failed out of 46 > > so I included libmkl_intel_lp64.so: > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl > -DCMAKE_INSTALL_PREFIX=$installDir > > -DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so" > -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib" > -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64 -L/usr/bin/gcc/lib64" > -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF > -DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc" > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc" > -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out > which doesn't give any error messages for cmake, but then in *sudo make -j > 4 *results in > > [ 46%] Building CXX object > src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o > icpc: error #10105: > > /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom: > core dumped > icpc: warning #10102: unknown signal(694380720) > icpc: error #10106: Fatal error in > > /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom, > terminated by unknown > compilation aborted for > /home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1) > src/gromacs/CMakeFiles/libgromacs.dir/build.make:2136: recipe for target > 'src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o' failed > make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o] > Error 1 > make[2]: *** Waiting for unfinished jobs > CMakeFiles/Makefile2:2499: recipe for target > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > Makefile:162: recipe for target 'all' failed > make: *** [all] Error 2 > Thanks for any help > > > On Tue, Oct 8, 2019 at 2:21 AM Paul bauer wrote: > > > Hej, > > > > I can't access the repository, so I can't say for certain what happened. > > Can you share your cmake command line? > > > > Cheers > > > > Paul > > > > On 07/10/2019 21:25, Lyudmyla Dorosh wrote: > > > Hello Gromacs Developers/Users, > > > > > > I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel > > > compilers (+MKL+MPI). > > > First I compiled cmake with Intel compilers. All output files are > > attached. > > > cmake, make seemed to go ok, but all check test failed. What do I do > > wrong? > > > > > > https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn/view?usp=sharing > > > > > > Thank you, > > > > > > Lyudmyla Dorosh, PhD > > > > > > University of Alberta > > > Department of Electrical and Computer Engineering, > > > 4-021 ECERF > > > Edmonton, AB, T6G 2G8 > > > Canada > > > Email: dor...@ualberta.ca
Re: [gmx-users] Batch mode error in GROMACS version 2019.2
That makes sense. Thanks, a lot. On Sun, Sep 15, 2019 at 4:53 PM Mark Abraham wrote: > Hi, > > I can imagine some MPI setups would control whether and how the shell > streams used in such redirections are passed through, so the fact that gmx > works and gmx_mpi doesn't seems consistent. Use gmx if you need scripting. > You only need the MPI build for running mdrun, so you'll have a good time > if you build your workflows around that notion. > > Mark > > On Sat, 14 Sep 2019 at 10:16, Rajib Biswas wrote: > > > Hi David, > > > > As I said in my previous email, when I am using > > > > echo 18 0 | gmx_mpi energy -f traj.edr -o temperature > > > > getting the following error: > > > > Program: gmx energy, version 2019.2 > > Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296) > > > > Fatal error: > > No energy terms selected > > > > > > However, if I use > > > > echo 18 0 | gmx_d energy -f traj.edr -o temperature > > > > There is no error. > > Note that for both the cases (i.e. gmx_mpi and gmx_d) interactive mode is > > working fine. > > > > > > Thanks. > > > > With regards, > > Rajib > > > > > > On Sat, Sep 14, 2019 at 12:56 PM David van der Spoel < > sp...@xray.bmc.uu.se > > > > > wrote: > > > > > Den 2019-09-14 kl. 08:36, skrev Rajib Biswas: > > > > I did some more experimentation about this and found that this error > is > > > > coming only with the mpi enabled version. > > > please give the exact command line > > > > > > > > Rajib > > > > > > > > On Fri, Sep 13, 2019 at 10:58 PM Rajib Biswas > > > wrote: > > > > > > > >> Hi Mark, > > > >> > > > >> Thanks! > > > >> > > > >> Interactively I could do it without any error. However, this error > > only > > > >> arises whenever I have tried to use batch mode. > > > >> > > > >> With regards, > > > >> *Rajib* > > > >> > > > >> > > > >> On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham < > > mark.j.abra...@gmail.com> > > > >> wrote: > > > >> > > > >>> What happens when you do it interactively? > > > >>> > > > >>> Mark > > > >>> > > > >>> On Fri, 13 Sep 2019 at 14:21, Rajib Biswas > > > wrote: > > > >>> > > > >>>> Dear All, > > > >>>> > > > >>>> I am trying to use the post-processing tools in batch mode. I am > > using > > > >>> the > > > >>>> following commands > > > >>>> > > > >>>> echo 18 0 | gmx_mpi energy -f traj.edr -o temperature > > > >>>> > > > >>>> Getting the following error: > > > >>>> > > > >>>> Program: gmx energy, version 2019.2 > > > >>>> Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296) > > > >>>> > > > >>>> Fatal error: > > > >>>> No energy terms selected > > > >>>> > > > >>>> > > > >>>> I have even tried all the options mentioned > > > >>>> > > > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > > >>>> however, could not get it worked for version 2019.2. > > > >>>> > > > >>>> Any help will be appreciated. > > > >>>> > > > >>>> With regards, > > > >>>> *Rajib* > > > >>>> -- > > > >>>> 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] Batch mode error in GROMACS version 2019.2
Hi David, As I said in my previous email, when I am using echo 18 0 | gmx_mpi energy -f traj.edr -o temperature getting the following error: Program: gmx energy, version 2019.2 Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296) Fatal error: No energy terms selected However, if I use echo 18 0 | gmx_d energy -f traj.edr -o temperature There is no error. Note that for both the cases (i.e. gmx_mpi and gmx_d) interactive mode is working fine. Thanks. With regards, Rajib On Sat, Sep 14, 2019 at 12:56 PM David van der Spoel wrote: > Den 2019-09-14 kl. 08:36, skrev Rajib Biswas: > > I did some more experimentation about this and found that this error is > > coming only with the mpi enabled version. > please give the exact command line > > > > Rajib > > > > On Fri, Sep 13, 2019 at 10:58 PM Rajib Biswas > wrote: > > > >> Hi Mark, > >> > >> Thanks! > >> > >> Interactively I could do it without any error. However, this error only > >> arises whenever I have tried to use batch mode. > >> > >> With regards, > >> *Rajib* > >> > >> > >> On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham > >> wrote: > >> > >>> What happens when you do it interactively? > >>> > >>> Mark > >>> > >>> On Fri, 13 Sep 2019 at 14:21, Rajib Biswas > wrote: > >>> > >>>> Dear All, > >>>> > >>>> I am trying to use the post-processing tools in batch mode. I am using > >>> the > >>>> following commands > >>>> > >>>> echo 18 0 | gmx_mpi energy -f traj.edr -o temperature > >>>> > >>>> Getting the following error: > >>>> > >>>> Program: gmx energy, version 2019.2 > >>>> Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296) > >>>> > >>>> Fatal error: > >>>> No energy terms selected > >>>> > >>>> > >>>> I have even tried all the options mentioned > >>>> > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > >>>> however, could not get it worked for version 2019.2. > >>>> > >>>> Any help will be appreciated. > >>>> > >>>> With regards, > >>>> *Rajib* > >>>> -- > >>>> 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. > >>> > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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] Batch mode error in GROMACS version 2019.2
I did some more experimentation about this and found that this error is coming only with the mpi enabled version. Rajib On Fri, Sep 13, 2019 at 10:58 PM Rajib Biswas wrote: > Hi Mark, > > Thanks! > > Interactively I could do it without any error. However, this error only > arises whenever I have tried to use batch mode. > > With regards, > *Rajib* > > > On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham > wrote: > >> What happens when you do it interactively? >> >> Mark >> >> On Fri, 13 Sep 2019 at 14:21, Rajib Biswas wrote: >> >> > Dear All, >> > >> > I am trying to use the post-processing tools in batch mode. I am using >> the >> > following commands >> > >> > echo 18 0 | gmx_mpi energy -f traj.edr -o temperature >> > >> > Getting the following error: >> > >> > Program: gmx energy, version 2019.2 >> > Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296) >> > >> > Fatal error: >> > No energy terms selected >> > >> > >> > I have even tried all the options mentioned >> > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts >> > however, could not get it worked for version 2019.2. >> > >> > Any help will be appreciated. >> > >> > With regards, >> > *Rajib* >> > -- >> > 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. >> > -- 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] Batch mode error in GROMACS version 2019.2
Hi Mark, Thanks! Interactively I could do it without any error. However, this error only arises whenever I have tried to use batch mode. With regards, *Rajib* On Fri, Sep 13, 2019 at 6:06 PM Mark Abraham wrote: > What happens when you do it interactively? > > Mark > > On Fri, 13 Sep 2019 at 14:21, Rajib Biswas wrote: > > > Dear All, > > > > I am trying to use the post-processing tools in batch mode. I am using > the > > following commands > > > > echo 18 0 | gmx_mpi energy -f traj.edr -o temperature > > > > Getting the following error: > > > > Program: gmx energy, version 2019.2 > > Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296) > > > > Fatal error: > > No energy terms selected > > > > > > I have even tried all the options mentioned > > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > however, could not get it worked for version 2019.2. > > > > Any help will be appreciated. > > > > With regards, > > *Rajib* > > -- > > 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. > -- 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] Batch mode error in GROMACS version 2019.2
Dear All, I am trying to use the post-processing tools in batch mode. I am using the following commands echo 18 0 | gmx_mpi energy -f traj.edr -o temperature Getting the following error: Program: gmx energy, version 2019.2 Source file: src/gromacs/gmxana/gmx_energy.cpp (line 296) Fatal error: No energy terms selected I have even tried all the options mentioned http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts however, could not get it worked for version 2019.2. Any help will be appreciated. With regards, *Rajib* -- 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.
