Hi, *>> Please try the latest 5.0.4 release, we might well have fixed a bug in the template compilation stuff.*
I just tried 5.0.4 and have the same error. *>> Even then, per the README you will find in share/template, you will might have to teach CMake that it should augment the linking path.* Sorry I do not quite understand what it means. Could you please explain a bit more specific on what I should do next? Thanks for your time. Sincerely, Qian On Tue, Apr 14, 2015 at 12:34 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, Apr 14, 2015 at 4:15 PM, qian wang <qq.wang...@gmail.com> wrote: > > > Hi, > > > > Here is the information. Thank you. > > > > cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on > > -DCMAKE_PREFIX_PATH=/usr/lib64: > > .... > > Looking for sgemm_ > > -- Looking for sgemm_ - found > > -- A library with BLAS API found. > > -- Looking for cheev_ > > -- Looking for cheev_ - found > > -- A library with LAPACK API found. > > -- Checking for dlopen > > -- Performing Test HAVE_DLOPEN > > -- Performing Test HAVE_DLOPEN - Success > > -- Checking for dlopen - found > > -- Found the ability to use plug-ins when building shared libaries, so > will > > compile to use plug-ins (e.g. to read VMD-supported file formats) > > ..... > > Configuring done > > > > OK, it did find your LAPACK. > > > > make > > ..... > > Linking CXX executable ../../bin/template > > /usr/bin/c++ -march=core-avx2 -std=c++0x -Wextra > > -Wno-missing-field-initializers -Wpointer-arith -Wall > > -Wno-unused-function -fomit-frame-pointer -funroll-all-loops > > -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG > > CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic > > ../../lib/libgromacs.so.0.0.0 -fopenmp -ldl -lrt -lm -lfftw3f -lblas > > -llapack -lblas -llapack -lpthread > > -Wl,-rpath,/home/qw9/Downloads/gromacs-5.0/build/lib > > ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' > > collect2: error: ld returned 1 exit status > > make[2]: *** [bin/template] Error 1 > > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 > > make: *** [all] Error 2 > > > > That works for me (i.e. the linker line has system BLAS and LAPACK > libraries). Please try the latest 5.0.4 release, we might well have fixed a > bug in the template compilation stuff. > > In any case, in 5.0.x the intended use case for the template is to install > GROMACS, and then copy the installed template machinery somewhere so you > can use it. Even then, per the README you will find in share/template, you > will might have to teach CMake that it should augment the linking path. > > Mark > > > > Sincerely, > > Qian > > > > On Tue, Apr 14, 2015 at 3:56 AM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > When you ran cmake originally, what did it report about which LAPACK it > > > found and will use? (You may need to clean your build tree and start > > again > > > in order to find this out.) What is the linker command line now (e.g. > > make > > > VERBOSE=1) > > > > > > Mark > > > > > > On Mon, Apr 13, 2015 at 11:30 PM, qian wang <qq.wang...@gmail.com> > > wrote: > > > > > > > Dear All, > > > > > > > > I am a new user of gromacs 5.0. For my own purposes I made small > > changes > > > in > > > > a gromacs source code where I called a function named "DPOTRF". This > > is a > > > > standard function in LAPACK library but not in the gromacs internal > > > LAPACK > > > > library. > > > > > > > > Now I have a problem of compiling. What I did is: > > > > > > > > cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on > > > > -DCMAKE_PREFIX_PATH=/usr/lib64 (this is the path of my extenal LAPACK > > > > library) > > > > this step is ok > > > > but next when I "make", the error I got is: > > > > > > > > Linking CXX executable ../../bin/template > > > > ../../lib/libgromacs.so.0.0.0: undefined reference to `dpotrf' > > > > collect2: error: ld returned 1 exit status > > > > make[2]: *** [bin/template] Error 1 > > > > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 > > > > > > > > Could anyone help me with this problem? Thanks a lot. > > > > > > > > Sincerely, > > > > Qian > > > > -- > > > > 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? 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