[gmx-users] How to call an external LAPACK function in gromacs

[qian wang]

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.abraham at gmail.com>
wrote:

> Hi,
>
> On Tue, Apr 14, 2015 at 4:15 PM, qian wang <qq.wang630 at 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.abraham at 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.wang630 at 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
> > > > --
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