[gmx-users] problem install gromacs in parallel

Gaurav Goel gauravgoeluta at gmail.com
Wed Jun 23 15:02:44 CEST 2010 

I'm trying to install a local copy of GROMACS on Ohio Super Computer.
I was able to build single and double precision versions (did make
distclean after each), however, got errors while installing parallel
version.

I will appreciate you taking time to help with this installation. Thanks.

This is what I did:

export CPPFLAGS=$FFTW_CFLAGS
export LDFLAGS=$FFTW_LIBS

****contents of FFTW_CFLAGS=-I/usr/local/fftw3-3.1.2/include
fftw3.f  fftw3.h

***contents of FFTW_LIBS=-L/usr/local/fftw3-3.1.2/lib -lfftw3 -lfftw3f -lm
libfftw3.a    libfftw3f.so        libfftw3.la    libfftw3.so.3.1.2
libfftw3f.a   libfftw3f.so.3      libfftw3.so    pkgconfig
libfftw3f.la  libfftw3f.so.3.1.2  libfftw3.so.3

***output from './configure --enable-mpi
--prefix=/nfs/18/cwr0350/my_gromacs/gromacs_1_bin
--program-suffix=_mpi &>config.out'

checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... gcc3
checking for mpxlc... no
checking for mpicc... mpicc
checking whether the MPI cc command works... yes
checking for catamount... no
checking how to run the C preprocessor... mpicc -E
checking whether mpicc accepts -O3... yes
checking whether mpicc accepts -funroll-all-loops... no
checking whether mpicc accepts -std=gnu99... no
checking whether mpicc accepts  -fast -pc 32 -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused... no
*******************************************************************
* Sorry, these optimization settings don't seem to work for       *
* your C compiler. Use make CFLAGS=..., or edit the top Makefile. *
*******************************************************************
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking for int... yes
checking size of int... 4
checking for long int... yes
checking size of long int... 8
checking for long long int... yes
checking size of long long int... 8
checking for off_t... yes
checking size of off_t... 8
checking that size_t can hold pointers... yes
checking floating-point format... IEEE754 (little-endian byte and word order)
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from mpicc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC
checking if mpicc PIC flag -fPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... pgcc-Warning-Unknown
switch: -print-search-dirs
/usr/lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3f... yes
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking for rpc/xdr.h... yes
checking for xdr_float in -lnsl... yes
checking for working memcmp... yes
checking return type of signal handlers... void
checking for off_t... (cached) yes
checking for vprintf... yes
checking for _doprnt... no
checking if malloc debugging is wanted... no
checking for strcasecmp... yes
checking for strdup... yes
checking for bool... no
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for main in -lxml2... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for uid_t in sys/types.h... yes
checking for inline... inline
checking whether your compiler can handle assembly files (*.s)... yes
checking whether as fully supports X86_64 SSE instructions... yes
checking whether byte ordering is bigendian... (cached) no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/gmxlib/Makefile
config.status: creating src/gmxlib/gmx_blas/Makefile
config.status: creating src/gmxlib/gmx_lapack/Makefile
config.status: creating src/gmxlib/nonbonded/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile
config.status: creating include/Makefile
config.status: creating include/types/Makefile
config.status: creating src/mdlib/Makefile
config.status: creating src/kernel/Makefile
config.status: creating src/tools/Makefile
config.status: creating src/ngmx/Makefile
config.status: creating src/contrib/Makefile
config.status: creating scripts/Makefile
config.status: creating admin/Makefile
config.status: creating share/Makefile
config.status: creating share/tutor/Makefile
config.status: creating share/tutor/gmxdemo/Makefile
config.status: creating share/tutor/nmr1/Makefile
config.status: creating share/tutor/nmr2/Makefile
config.status: creating share/tutor/water/Makefile
config.status: creating share/tutor/mixed/Makefile
config.status: creating share/tutor/methanol/Makefile
config.status: creating share/tutor/speptide/Makefile
config.status: creating share/template/Makefile
config.status: creating share/top/Makefile
config.status: creating share/html/Makefile
config.status: creating share/html/images/Makefile
config.status: creating share/html/online/Makefile
config.status: creating man/Makefile
config.status: creating man/man1/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands

* On most platforms you can save 10X space with dynamic libraries, although
  the binaries might be less portable. Why not try --enable-shared ?

*******output from make mdrun &> log
(cd ./src/gmxlib && make ; exit 0)
make[1]: Entering directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib'
Making all in nonbonded
make[2]: Entering directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded'
Making all in nb_kernel_x86_64_sse
make[3]: Entering directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel_x86_64_sse'
/bin/sh ../../../../libtool --tag=CC   --mode=link mpicc
-L/usr/local/fftw3-3.1.2/lib -lfftw3 -lfftw3f -lm   -o
libnb_kernel_x86_64_sse.la  nb_kernel010_x86_64_sse.lo
nb_kernel030_x86_64_sse.lo nb_kernel100_x86_64_sse.lo
nb_kernel101_x86_64_sse.lo nb_kernel102_x86_64_sse.lo
nb_kernel103_x86_64_sse.lo nb_kernel104_x86_64_sse.lo
nb_kernel110_x86_64_sse.lo nb_kernel111_x86_64_sse.lo
nb_kernel112_x86_64_sse.lo nb_kernel113_x86_64_sse.lo
nb_kernel114_x86_64_sse.lo nb_kernel130_x86_64_sse.lo
nb_kernel131_x86_64_sse.lo nb_kernel132_x86_64_sse.lo
nb_kernel133_x86_64_sse.lo nb_kernel134_x86_64_sse.lo
nb_kernel200_x86_64_sse.lo nb_kernel201_x86_64_sse.lo
nb_kernel202_x86_64_sse.lo nb_kernel203_x86_64_sse.lo
nb_kernel204_x86_64_sse.lo nb_kernel210_x86_64_sse.lo
nb_kernel211_x86_64_sse.lo nb_kernel212_x86_64_sse.lo
nb_kernel213_x86_64_sse.lo nb_kernel214_x86_64_sse.lo
nb_kernel230_x86_64_sse.lo nb_kernel231_x86_64_sse.lo
nb_kernel232_x86_64_sse.lo nb_kernel233_x86_64_sse.lo
nb_kernel234_x86_64_sse.lo nb_kernel300_x86_64_sse.lo
nb_kernel301_x86_64_sse.lo nb_kernel302_x86_64_sse.lo
nb_kernel303_x86_64_sse.lo nb_kernel304_x86_64_sse.lo
nb_kernel310_x86_64_sse.lo nb_kernel311_x86_64_sse.lo
nb_kernel312_x86_64_sse.lo nb_kernel313_x86_64_sse.lo
nb_kernel314_x86_64_sse.lo nb_kernel330_x86_64_sse.lo
nb_kernel331_x86_64_sse.lo nb_kernel332_x86_64_sse.lo
nb_kernel333_x86_64_sse.lo nb_kernel334_x86_64_sse.lo
nb_kernel400_x86_64_sse.lo nb_kernel410_x86_64_sse.lo
nb_kernel430_x86_64_sse.lo nb_kernel_x86_64_sse_test_asm.lo
nb_kernel_x86_64_sse.lo  -lxml2  -lnsl -lfftw3f -lm   -lSM -lICE -lX11
mkdir .libs
ar cru .libs/libnb_kernel_x86_64_sse.a  nb_kernel010_x86_64_sse.o
nb_kernel030_x86_64_sse.o nb_kernel100_x86_64_sse.o
nb_kernel101_x86_64_sse.o nb_kernel102_x86_64_sse.o
nb_kernel103_x86_64_sse.o nb_kernel104_x86_64_sse.o
nb_kernel110_x86_64_sse.o nb_kernel111_x86_64_sse.o
nb_kernel112_x86_64_sse.o nb_kernel113_x86_64_sse.o
nb_kernel114_x86_64_sse.o nb_kernel130_x86_64_sse.o
nb_kernel131_x86_64_sse.o nb_kernel132_x86_64_sse.o
nb_kernel133_x86_64_sse.o nb_kernel134_x86_64_sse.o
nb_kernel200_x86_64_sse.o nb_kernel201_x86_64_sse.o
nb_kernel202_x86_64_sse.o nb_kernel203_x86_64_sse.o
nb_kernel204_x86_64_sse.o nb_kernel210_x86_64_sse.o
nb_kernel211_x86_64_sse.o nb_kernel212_x86_64_sse.o
nb_kernel213_x86_64_sse.o nb_kernel214_x86_64_sse.o
nb_kernel230_x86_64_sse.o nb_kernel231_x86_64_sse.o
nb_kernel232_x86_64_sse.o nb_kernel233_x86_64_sse.o
nb_kernel234_x86_64_sse.o nb_kernel300_x86_64_sse.o
nb_kernel301_x86_64_sse.o nb_kernel302_x86_64_sse.o
nb_kernel303_x86_64_sse.o nb_kernel304_x86_64_sse.o
nb_kernel310_x86_64_sse.o nb_kernel311_x86_64_sse.o
nb_kernel312_x86_64_sse.o nb_kernel313_x86_64_sse.o
nb_kernel314_x86_64_sse.o nb_kernel330_x86_64_sse.o
nb_kernel331_x86_64_sse.o nb_kernel332_x86_64_sse.o
nb_kernel333_x86_64_sse.o nb_kernel334_x86_64_sse.o
nb_kernel400_x86_64_sse.o nb_kernel410_x86_64_sse.o
nb_kernel430_x86_64_sse.o nb_kernel_x86_64_sse_test_asm.o
nb_kernel_x86_64_sse.o
ranlib .libs/libnb_kernel_x86_64_sse.a
creating libnb_kernel_x86_64_sse.la
(cd .libs && rm -f libnb_kernel_x86_64_sse.la && ln -s
../libnb_kernel_x86_64_sse.la libnb_kernel_x86_64_sse.la)
make[3]: Leaving directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel_x86_64_sse'
Making all in nb_kernel
make[3]: Entering directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel'
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb.o mknb.c
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_metacode.o mknb_metacode.c
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_common.o mknb_common.c
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_declarations.o
mknb_declarations.c
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_outerloop.o mknb_outerloop.c
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_innerloop.o mknb_innerloop.c
cc -DHAVE_CONFIG_H -I. -I../../../../src -c -o mknb_interactions.o
mknb_interactions.c
cc -DHAVE_CONFIG_H -I. -I../../../../src -o mknb mknb.o
mknb_metacode.o mknb_common.o mknb_declarations.o mknb_outerloop.o
mknb_innerloop.o mknb_interactions.o
rm -f kernel-stamp
./mknb  -software_invsqrt
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating single precision functions in C.
>>> Using Gromacs software version of 1/sqrt(x).

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make  all-am
make[4]: Entering directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel'
/bin/sh ../../../../libtool --tag=CC   --mode=compile mpicc
-DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2
-I../../../../include
-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"
-I/usr/local/fftw3-3.1.2/include   -MT nb_kernel.lo -MD -MP -MF
.deps/nb_kernel.Tpo -c -o nb_kernel.lo nb_kernel.c
 mpicc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2
-I../../../../include
-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"
-I/usr/local/fftw3-3.1.2/include -MT nb_kernel.lo -MD -MP -MF
.deps/nb_kernel.Tpo -c nb_kernel.c -o nb_kernel.o
pgcc-Warning-Unknown switch: -MT
pgcc-Warning-Unknown switch: -MP
pgcc-Warning-Unknown switch: -MF
File with unknown suffix passed to linker: .deps/nb_kernel.Tpo
nb_kernel.c:
mv -f .deps/nb_kernel.Tpo .deps/nb_kernel.Plo
mv: cannot stat `.deps/nb_kernel.Tpo': No such file or directory
make[4]: *** [nb_kernel.lo] Error 1
make[4]: Leaving directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel'
make[3]: *** [all] Error 2
make[3]: Leaving directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded/nb_kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib/nonbonded'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory `/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/mdlib'
/bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H
-I. -I../../src -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"
-I/usr/local/fftw3-3.1.2/include   -MT calcvir.lo -MD -MP -MF
.deps/calcvir.Tpo -c -o calcvir.lo calcvir.c
 mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
-I../../include
-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"
-I/usr/local/fftw3-3.1.2/include -MT calcvir.lo -MD -MP -MF
.deps/calcvir.Tpo -c calcvir.c -o calcvir.o
pgcc-Warning-Unknown switch: -MT
pgcc-Warning-Unknown switch: -MP
pgcc-Warning-Unknown switch: -MF
File with unknown suffix passed to linker: .deps/calcvir.Tpo
calcvir.c:
mv -f .deps/calcvir.Tpo .deps/calcvir.Plo
mv: cannot stat `.deps/calcvir.Tpo': No such file or directory
make[1]: *** [calcvir.lo] Error 1
make[1]: Leaving directory `/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory
`/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/kernel'
mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
-I../../include
-DGMXLIBDIR=\"/nfs/18/cwr0350/my_gromacs/gromacs_1_bin/share/top\"
-I/usr/local/fftw3-3.1.2/include   -MT glaasje.o -MD -MP -MF
.deps/glaasje.Tpo -c -o glaasje.o glaasje.c
pgcc-Warning-Unknown switch: -MT
pgcc-Warning-Unknown switch: -MP
pgcc-Warning-Unknown switch: -MF
pgcc-Error-Output would overwrite input file: glaasje.o
make[1]: *** [glaasje.o] Error 1
make[1]: Leaving directory `/nfs/18/cwr0350/my_gromacs/gromacs-4.0.5/src/kernel'

-Gaurav

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