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). Progress: 1% Progress: 2% Progress: 4% Progress: 5% Progress: 7% Progress: 8% Progress: 10% Progress: 11% Progress: 13% Progress: 14% Progress: 16% Progress: 17% Progress: 19% Progress: 20% Progress: 22% Progress: 23% Progress: 25% Progress: 26% Progress: 28% Progress: 29% Progress: 31% Progress: 32% Progress: 34% Progress: 35% Progress: 37% Progress: 38% Progress: 40% Progress: 41% Progress: 43% Progress: 44% Progress: 46% Progress: 47% Progress: 49% Progress: 50% Progress: 52% Progress: 53% Progress: 55% Progress: 56% Progress: 58% Progress: 59% Progress: 61% Progress: 62% Progress: 64% Progress: 65% Progress: 67% Progress: 68% Progress: 70% Progress: 71% Progress: 73% Progress: 74% Progress: 76% Progress: 77% Progress: 79% Progress: 80% Progress: 82% Progress: 83% Progress: 85% Progress: 86% Progress: 88% Progress: 89% Progress: 91% Progress: 92% Progress: 94% Progress: 95% Progress: 97% Progress: 98% Progress: 100% 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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