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

[qian wang]

Hi,

I just found that changing from "dpotrf" to "dpotrf_" in the source code
would solve the problem... sorry for the trouble.

Sincerely,
Qian

On Tue, Apr 14, 2015 at 3:11 PM, qian wang <qq.wang630 at gmail.com> wrote:

> 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
>> > > > --
>> > > > 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-request at 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-request at 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-request at 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-request at gromacs.org.
>>
>
>