Re: [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0
On Sat, Apr 4, 2020 at 10:41 PM Wei-Tse Hsu wrote: > Dear gmx users, > Recently I've been trying to install GROMACS 2020.1. However, I encounter a > compilation error while using the make command. The error is as follows: > > > > > > */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find > /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit > statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** > [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* > From the error above, it seemed that GROMACS was unable to find library > like libpthread.so.0 and libpthread_nonshared.a. After checking I found > that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and > libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ > x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add > the paths of the libraries for GROMACS to search for. Specifically, the > command I was using is: > *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd > build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 > -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > As Kevin noted, the separator in the prefix path should be ";". However, it seem unnecessary to pass system libraries as custom paths to cmake. Try first without those. -- Szilárd > > gmx_compile.log* > However, it turned out that I still got the same error. I'm confused right > now since I thought that gromacs should be able to find the files. I'm > wondering if I missed something. Could someone please tell me what I can do > or share some relevant experience? Any help is much appreciated! > > Best, > Wei-Tse > -- > 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] Unable to compile GROMACS 2020.1 using GNU 7.5.0
Hi, I've had problems in the past with syntax requirements for CMAKE_PREFIX_PATH. Try putting the path in quotes and separating with a semicolon instead of a colon. Kevin On Sat, Apr 4, 2020 at 1:40 PM Wei-Tse Hsu wrote: > *Message sent from a system outside of UConn.* > > > Dear gmx users, > Recently I've been trying to install GROMACS 2020.1. However, I encounter a > compilation error while using the make command. The error is as follows: > > > > > > */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find > /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit > statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** > [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* > From the error above, it seemed that GROMACS was unable to find library > like libpthread.so.0 and libpthread_nonshared.a. After checking I found > that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and > libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ > x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add > the paths of the libraries for GROMACS to search for. Specifically, the > command I was using is: > *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd > build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 > -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > > gmx_compile.log* > However, it turned out that I still got the same error. I'm confused right > now since I thought that gromacs should be able to find the files. I'm > wondering if I missed something. Could someone please tell me what I can do > or share some relevant experience? Any help is much appreciated! > > Best, > Wei-Tse > -- > 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] Unable to compile GROMACS 2020.1 using GNU 7.5.0
Dear gmx users, Recently I've been trying to install GROMACS 2020.1. However, I encounter a compilation error while using the make command. The error is as follows: */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* >From the error above, it seemed that GROMACS was unable to find library like libpthread.so.0 and libpthread_nonshared.a. After checking I found that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add the paths of the libraries for GROMACS to search for. Specifically, the command I was using is: *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > gmx_compile.log* However, it turned out that I still got the same error. I'm confused right now since I thought that gromacs should be able to find the files. I'm wondering if I missed something. Could someone please tell me what I can do or share some relevant experience? Any help is much appreciated! Best, Wei-Tse -- 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.
