Hi,
thank you for pointing that out. I didn't actually know that sander will
not be built if I use a Cray compiler - perhaps the manual should be
more precise about that. Anyway, I successfully compiled AmberMD using
the Intel MPI wrapper on XC40.
Best regards,
Jakub
On 2020-08-04 15:32, Daniel Roe wrote:
> Hi,
>
> Unfortunately you're in uncharted waters here. I don't think any of
> the Amber devs have access to cray compilers anymore (I know I haven't
> for years). I'm pretty certain cmake was never tested with cray. You
> may want to try using the old legacy 'configure' script with the
> 'cray' compiler target. That did work for cray compilers on Blue
> Waters once upon a time, but that was a very long time ago now, and it
> results in a much smaller subset of Amber being compiled (you don't
> get sander for example).
>
> Sorry I can't help more; unless one of the other devs has access to
> cray compilers you may be in for a lot of trial and error.
>
> -Dan
>
> On Mon, Jul 27, 2020 at 6:28 PM Jakub Jalowiec <jj358817.icm.edu.pl>
> wrote:
>>
>> Dear Amber community,
>> I am trying to compile AmberMD with the -mpi flag enabled on an Intel
>> Haswell Cray XC40 using Cray compilers. I am using MPICH
>> (cray-mpich/7.7.10). Take a look at my compilers:
>>
>> > jj358817.nid00392:~/MM/amber/amber/amber20_src/build> which cc
>> > /opt/cray/pe/craype/2.6.1/bin/cc
>> > jj358817.nid00392:~/MM/amber/amber/amber20_src/build> which CC
>> > /opt/cray/pe/craype/2.6.1/bin/CC
>> > jj358817.nid00392:~/MM/amber/amber/amber20_src/build> which ftn
>> > /opt/cray/pe/craype/2.6.1/bin/ftn
>>
>> Moreover cc, CC and ftn are all MPI wrappers (i.e. I can compile MPI
>> code using them just fine).
>>
>> The cmake flags I'm using (amber20_src/build/run_cmake) look like this
>> (as far as I understand I had to pass -DMPI_C_LIBRARIES and
>> -DMPI_C_INCLUDE_PATH to MPICH directories so cc, CC and ftn are
>> properly
>> recognised as MPI wrappers):
>>
>> > cmake $AMBER_PREFIX/amber20_src \
>> > -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
>> > -DCOMPILER=CRAY \
>> > -DMPI=TRUE -DCUDA=FALSE -DINSTALL_TESTS=TRUE
>> > -DMPI_C_LIBRARIES=/opt/cray/pe/mpt/7.7.10/gni/mpich-crayclang/9.0/lib/
>> > -DMPI_C_INCLUDE_PATH=/opt/cray/pe/mpt/7.7.10/gni/mpich-crayclang/9.0/include/
>> > \
>> > -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE
>> > -DCMAKE_VERBOSE_MAKEFILE=TRUE \
>> > 2>&1 | tee cmake.log
>>
>> When I do ./run_cmake in that directory I get:
>> > jj358817.nid00392:~/MM/amber/amber/amber20_src/build> ./run_cmake
>> > --
>> > **************************************************************************
>> > -- Starting configuration of Amber version 20.0.0...
>> > -- CMake Version: 3.10.2
>> > -- For how to use this build system, please read this wiki:
>> > -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
>> > -- For a list of important CMake variables, check here:
>> > -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
>> > --
>> > **************************************************************************
>> > -- Amber source not found, only building AmberTools
>> > -- Cray Programming Environment 2.6.1 Fortran
>> > -- Testing if stdlib.h can be included...
>> > -- Testing if stdlib.h can be included... yes
>> > WARNING: Target "cmTC_e0684" requests linking to directory
>> > "/opt/cray/pe/mpt/7.7.10/gni/mpich-crayclang/9.0/lib/". Targets may
>> > link only to libraries. CMake is dropping the item.
>> > -- MPI C Compiler: /opt/cray/pe/craype/2.6.1/bin/cc
>> > -- MPI CXX Compiler: /opt/cray/pe/craype/2.6.1/bin/CC
>> > -- MPI Fortran Compiler: /opt/cray/pe/craype/2.6.1/bin/ftn
>> > -- If these are not the correct MPI wrappers, then set
>> > MPI_<language>_COMPILER to the correct wrapper and reconfigure.
>> > CMake Error at cmake/LibraryTracking.cmake:174 (message):
>> > Incorrect usage. At least one LIBRARY should be provided.
>> > Call Stack (most recent call first):
>> > cmake/MPIConfig.cmake:122 (import_libraries)
>> > CMakeLists.txt:118 (include)
>>
>> The error message "Incorrect usage. At least one LIBRARY should be
>> provided." is undescriptive. :( I tried to hunt down the cause of that
>> error by myself trying to debug cmake/LibraryTracking.cmake but failed
>> as I am new to CMake. I am stuck now. Can you please guide me in
>> resolving that problem?
>>
>> Best regards,
>> Jakub
>>
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>
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Received on Wed Aug 12 2020 - 02:00:02 PDT
