[gmx-users] Cannot link to SIMD version when installing GMX4.6.6 on BG/P

[lina]

Here is the complete version I used:

cmake .. \
    -DCMAKE_SYSTEM_NAME=BlueGene \
    -DCMAKE_INSTALL_PREFIX=/home/lina \
    -DGMX_MPI=ON \
    -DCMAKE_CXX_COMPILER=bgxlc++ \
    -DCMAKE_C_COMPILER=/bgsys/drivers/ppcfloor/comm/xl/bin/mpixlc \
    -DCMAKE_C_FLAGS="-O3 -qnostaticlink
-L/opt/ibmcmp/xlmass/bg/7.3/bglib64 -lmass_simd" \
    -DFFTWF_LIBRARY=/scratch/home/lina/lib/libfftw3f.so \
    -DFFTWF_INCLUDE_DIR=/scratch/home/lina/include


Additionally, below one is for the FFTW instalation

$ more fftw-configure-mpi.sh
#!/bin/bash
    ./configure     CC="bgxlc"  \
            CXX="bgxlc++" \
            MPICC="/bgsys/drivers/ppcfloor/comm/xl/bin/mpixlc" \
            F77="bgf77" \
            CFLAGS="-O3 -qnostaticlink  " \
            --enable-single  \
               --enable-mpi \
            --enable-shared \
            --prefix=/home/lina

HTH,

P.S.

During `make` I met something, such as:

1] 1506-1354 (W) Option -qsmp should be used with option -qthreaded.
 2] /opt/ibmcmp/vac/bg/12.1/bin/.orig/bgxlc: 1501-218 (W) file
CMakeFiles/g_pme_error.dir/g_pme_error.c.obj contains an incorrect
file suffix
3] 1500-030: (I) INFORMATION: gmx_dos: Additional optimization may be
attained by recompiling and specifying MAXMEM option with a value
greater than 8192.
    1500-030: (I) INFORMATION: gmx_editconf: Additional optimization
may be attained by recompiling and specifying MAXMEM option with a
value greater than 8192.
    1500-030: (I) INFORMATION: gmx_hbond: Additional optimization may
be attained by recompiling and specifying MAXMEM option with a value
greater than 8192.
    1441  1500-010: (W) WARNING in gmx_trjconv: Infinite loop.
Program may not stop.
    1500-030: (I) INFORMATION: gmx_trjconv: Additional optimization
may be attained by recompiling and specifying MAXMEM option with a
value greater than 8192.
    1500-030: (I) INFORMATION: gmx_bar: Additional optimization may be
attained by recompiling and specifying MAXMEM option with a value
greater than 8192.

On Fri, Jul 18, 2014 at 3:38 PM, lina <lina.lastname at gmail.com> wrote:
> Hi,
>
> Have you fixed the problem?
>
> On BG/Q, Version  4.6.5.
>
> Here, the /libmass_simd.a is under /opt/ibmcmp/xlmass/bg/7.3/bglib64
> (it may different from yours).
>
> During cmake I added
>
> -DCMAKE_C_FLAGS="-O3 -L/opt/ibmcmp/xlmass/bg/7.3/bglib64 -lmass_simd"
>
> It works on my side, you may do a check by yourself. Please also pay
> attention to the compiler you use. XL is different.
>
> Good luck,
>
>
> On Wed, Jul 9, 2014 at 3:49 AM, Xingcheng Lin
> <linxingcheng50311 at gmail.com> wrote:
>> Hi,
>>
>> I have some problem installing GMX4.6.6 on BG/P, the error is as follows:
>>
>> -- Looking for atan2f4 in mass_simd
>> -- Looking for atan2f4 in mass_simd - not found
>> CMake Error at CMakeLists.txt:1082 (message):
>>   Could not link to the SIMD version of the IBM MASS library.  Please adjust
>>   your CMAKE_PREFIX_PATH to contain it
>>
>> The CMAKE_PREFIX_PATH I used is the prefix for fftw, as suggested from
>> http://www.gromacs.org/Documentation/Installation_Instructions#bluegenep
>>
>> The website also suggests: "There is currently no SIMD support on this
>> platform and no plans to add it. The default plain C kernels will work."
>>
>> It seems I should not include SIMD when compiling, but I am not pretty sure
>> how to do that, -DGMX_SIMD=NONE doesn't help.
>>
>> Anyone knows how to do that?
>> --
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>>
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