[gmx-users] Problem compiling Gromacs 5.1 with XL Compiler

[Mark Abraham]

Hi,

That all seems wildly unlikely, particularly as you say you can compile
earlier GROMACS versions with the same toolchain. The errors are caused by
the compiler interpreting gmx_unused as a variable name, instead of a
portable way to suppress compiler warnings about variables that are unused
on some code paths. But the source file is correctly including the header
that declares gmx_unused (and in any case, if there was a compiler problem,
gmx_unused should preprocess to something that triggers a different
compiler error, or to nothing).

Can you please email me (off list) your CMakeCache.txt, src/config.h
src/buildinfo.h from the build directory?

Thanks,

Mark


On Mon, Aug 17, 2015 at 8:43 AM Jernej Zidar <jernej.zidar at gmail.com> wrote:

> Hi,
>   I am unable to compile Gromacs 5.1 using the XL compiler (version 12.1.0)
> on our BlueGene/Q cluster.
>
>   Before starting I set the relevant paths like so:
> export PATH=/bgsys/drivers/ppcfloor/comm/xl/bin/:$PATH
> export
> LD_LIBRARY_PATH=/bgsys/drivers/ppcfloor/comm/xl/lib/:$LD_LIBRARY_PATH
> export CXX=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicxx
> export CC=/bgsys/drivers/ppcfloor/comm/xl/bin/mpicc
>
>   Gromacs is configured like so:
> cmake ../gromacs-5.1 \
> -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C \-DGMX_MPI=ON \
> -DCMAKE_INSTALL_PREFIX=/home/ihpczidj/scratch/ \
> -DGMX_BUILD_OWN_FFTW=ON -DGMX_BUILD_MDRUN_ONLY=ON
>
>   The whole list of errors:
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 181.76: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 201.79: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 281.72: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 302.75: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1472.77: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1486.80: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1575.73: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1589.76: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2810.92: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2824.95: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2904.88: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2918.91: 1540-0063 (S) The text "m" is unexpected.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 326.36: 1540-0274 (S) The name lookup for "gmx_simd_invsqrt_notmaskfpe_f"
> did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 541.15: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_f" did
> not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 688.15: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_f" did
> not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 999.37: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_f" did not
> find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1031.32: 1540-0274 (S) The name lookup for "gmx_simd_invsqrt_notmaskfpe_f"
> did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1080.31: 1540-0274 (S) The name lookup for "gmx_simd_invsqrt_notmaskfpe_f"
> did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1120.34: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_f" did not
> find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1174.41: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_f" did
> not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1609.36: 1540-0274 (S) The name lookup for "gmx_simd_invsqrt_notmaskfpe_d"
> did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1851.40: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_d" did not
> find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 1887.41: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_d" did
> not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2036.40: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_d" did not
> find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2072.41: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_d" did
> not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2365.37: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_d" did not
> find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2474.34: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_d" did not
> find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2568.29: 1540-0274 (S) The name lookup for "gmx_simd_inv_maskfpe_d" did not
> find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2638.41: 1540-0274 (S) The name lookup for "gmx_simd_inv_notmaskfpe_d" did
> not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 2942.36: 1540-0274 (S) The name lookup for
> "gmx_simd_invsqrt_notmaskfpe_singleaccuracy_d" did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 3157.15: 1540-0274 (S) The name lookup for
> "gmx_simd_inv_notmaskfpe_singleaccuracy_d" did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 3279.15: 1540-0274 (S) The name lookup for
> "gmx_simd_inv_notmaskfpe_singleaccuracy_d" did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 3552.37: 1540-0274 (S) The name lookup for
> "gmx_simd_inv_maskfpe_singleaccuracy_d" did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 3585.32: 1540-0274 (S) The name lookup for
> "gmx_simd_invsqrt_notmaskfpe_singleaccuracy_d" did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 3635.31: 1540-0274 (S) The name lookup for
> "gmx_simd_invsqrt_notmaskfpe_singleaccuracy_d" did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 3675.34: 1540-0274 (S) The name lookup for
> "gmx_simd_inv_maskfpe_singleaccuracy_d" did not find a declaration.
> "/home/ihpczidj/scratch/gromacs-5.1/src/gromacs/simd/simd_math.h", line
> 3730.41: 1540-0274 (S) The name lookup for
> "gmx_simd_inv_notmaskfpe_singleaccuracy_d" did not find a declaration.
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o] Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
>   Any idea what could be causing this error? I was able to compile previous
> versions of Gromacs (4.6.x, 5.0.y) on the same hardware without a problem.
>
> Thanks,
> Jernej
> --
> 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.
>