[CP2K:2671] Re: compile the latest version of cp2k with g95

Axel akoh... at gmail.com
Wed Apr 21 13:19:36 UTC 2010


On Apr 21, 8:43 am, zh <vale... at gmail.com> wrote:
> Dear all,
>
> I tried to compile the latest version (e.g. 2.1.223) of cp2k with g95,
> scalapck (0.96), openmpi-1.4.1. The g95 installed on my computer
> cluster is the 0.92 version built on Linux x86_64/EMT64 (32 bit
> D.I.).  The fftw3, openmpi, and scalapack are compiled with this
> version of g95 and installed on my machines.The following arch file
> was used for compiling cp2k:

as you can see from the stack trace, the error
is coming from openmpi and thus unlikely to be
compiler dependent.

what you see on the XT5 is very likely a different issue.

axel.




> CC       = cc
> CPP      = /usr/bin/cpp
> FC       = /work/z-hou/soft/openmpi-g95/bin/mpif90
> LD       = /work/z-hou/soft/openmpi-g95/bin/mpif90
> AR       = ar -r
> DFLAGS   = -D__G95 -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK -
> D__FFTW3
> G95_INC  = /work/z-hou/soft/fftw3-g95/include
> CPPFLAGS = -C -traditional  $(DFLAGS) -I$(G95_INC)
> FCFLAGS  = $(DFLAGS) -I$(G95_INC) -ffree-form -fno-underscoring  -O1 -
> ffast-math -cpp -g -fbounds-check -ftrace=full   -funroll-loops
> LDFLAGS  = $(FCFLAGS)
> G95_LIB = /work/z-hou/scalapack_installer_0.96/lib
> LIBS     = $(G95_LIB)/libscalapack.a \
>            $(G95_LIB)/blacsC.a \
>            $(G95_LIB)/blacsF77.a \
>            $(G95_LIB)/blacs.a \
>            $(G95_LIB)/libreflapack.a \
>            $(G95_LIB)/librefblas.a \
>            /work/z-hou/soft/fftw3-g95/lib/libfftw3.a
>
> OBJECTS_ARCHITECTURE = machine_g95.o
>
> The binary module of cp2k (i.e., cp2k.popt) is successfully obtained
> with the above arch file. But when I run it in parallel manner, the
> following errors were met:
>
> [pcc-hs36:16109] *** Process received signal ***
> [pcc-hs36:16109] Signal: Segmentation fault (11)
> [pcc-hs36:16109] Signal code:  (128)
> [pcc-hs36:16109] Failing at address: (nil)
> [pcc-hs36:16109] [ 0] /lib64/libpthread.so.0 [0x382700e7c0]
> [pcc-hs36:16109] [ 1] /work/z-hou/soft/openmpi-g95/lib/libmpi.so.0
> [0x2b66ad6d1c9b]
> [pcc-hs36:16109] [ 2] /work/z-hou/soft/openmpi-g95/lib/libmpi.so.
> 0(PMPI_Group_incl+0x172) [0x2b66ad6f87d2]
> [pcc-hs36:16109] [ 3] /work/z-hou/bin/cp2k.sopt(BI_TransUserComm+0x52)
> [0x34957e2]
> [pcc-hs36:16109] [ 4] /work/z-hou/bin/cp2k.sopt(blacs_gridmap+0x10d)
> [0x348dc0d]
> [pcc-hs36:16109] [ 5] /work/z-hou/bin/cp2k.sopt(blacs_gridinit+0xbb)
> [0x348dadb]
> [pcc-hs36:16109] [ 6] /work/z-hou/bin/
> cp2k.sopt(cp_blacs_calls_MP_cp_blacs_gridinit+0x4c) [0x2cc830c]
> [pcc-hs36:16109] [ 7] /work/z-hou/bin/
> cp2k.sopt(cp_blacs_env_MP_cp_blacs_env_create+0x542) [0x1b1984a]
> [pcc-hs36:16109] [ 8] /work/z-hou/bin/
> cp2k.sopt(qs_environment_types_MP_init_qs_env+0x1098) [0xb1ef24]
> [pcc-hs36:16109] [ 9] /work/z-hou/bin/
> cp2k.sopt(qs_environment_types_MP_qs_env_create+0x122) [0xb21b4d]
> [pcc-hs36:16109] [10] /work/z-hou/bin/
> cp2k.sopt(qs_main_MP_quickstep_create_force_env+0x12b) [0xcff143]
> [pcc-hs36:16109] [11] /work/z-hou/bin/
> cp2k.sopt(f77_interface_MP_create_force_env+0x1c15) [0x4f515b]
> [pcc-hs36:16109] [12] /work/z-hou/bin/cp2k.sopt(cp2k_runs_MP_cp2k_run
> +0x1b83) [0x4afc53]
> [pcc-hs36:16109] [13] /work/z-hou/bin/cp2k.sopt(cp2k_runs_MP_run_input
> +0x24d) [0x4bab8b]
> [pcc-hs36:16109] [14] /work/z-hou/bin/cp2k.sopt(MAIN_+0x154b)
> [0x4ad1cb]
> [pcc-hs36:16109] [15] /work/z-hou/bin/cp2k.sopt(main+0xe) [0x366f97e]
> [pcc-hs36:16109] [16] /lib64/libc.so.6(__libc_start_main+0xf4)
> [0x382641d994]
> [pcc-hs36:16109] [17] /work/z-hou/bin/cp2k.sopt [0x4abbe9]
> [pcc-hs36:16109] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 16109 on node pcc-hs36
> exited on signal 11 (Segmentation fault).
> --------------------------------------------------------------------------
>
> From searching the solution of the similar problem on internet, it
> seems to be related to how fortran compiler handles the 32 bit and 64
> bit in mpi. But I did not find out the exact solution.
>
> I also tried the 0.92 version of g95 built on Linux x86_64/EMT64 (64
> bit D.I.). The same errors were met.  I also suffered this terrible
> problem when I used the intel fortran compiler on a same machine and
> the pgi fortran compiler on a CARY-XT5 machine to compile the latest
> version of cp2k. If anyone can give me some helps or hints to fix this
> problem, I will greatly appreciate him.
>
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