pgcc-Fatal-linker

Hi,
Ia m trying to compile ABINIT in parallel and am in need of some help.

I am coming across the following error when it tries to configure netcdf as a plugin:


checking FFLAGS… -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2
checking type /opt/vltmpi/OPENIB/mpi//bin/mpif90… /opt/vltmpi/OPENIB/mpi//bin/mpif90 is /opt/vltmpi/OPENIB/mpi//bin/mpif90
checking F90… unset
checking AR… ar
checking AR_FLAGS… cru
checking type ar… ar is /usr/bin/ar
checking NM… /usr/bin/nm -B
checking NMFLAGS…
checking for /usr/bin/nm… /usr/bin/nm -B
checking nm flags…
checking for C-equivalent to Fortran routine “SUB”… sub_
checking for Fortran “byte”… yes
checking for Fortran “integer*2”… yes
checking if Fortran “byte” is C “signed char”… configure: error: Could not link conftestf.o and conftest.o

On looking at the config.log for netcdf I get a lot of errors such as;

configure:3596: /opt/vltmpi/OPENIB/mpi//bin/mpicc --version >&5
pgcc-Warning-Unknown switch: --version
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’
configure:3600: $? = 2
configure:3607: /opt/vltmpi/OPENIB/mpi//bin/mpicc -v >&5
mpicc for 1.2.6 (release) of : 2004/09/20 12:35:29

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -lmpich -lmpichfstub -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’
pgcc-Fatal-linker completed with exit code 1




AND

configure:3896: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
PGC-S-0040-Illegal use of symbol, choke (conftest.c: 17)
PGC-W-0156-Type not specified, ‘int’ assumed (conftest.c: 17)
PGC/x86-64 Linux/x86-64 6.2-5: compilation completed with severe errors
configure:3903: $? = 2
configure: failed program was:
| /* confdefs.h. /
| #define PACKAGE_NAME “netCDF”
| #define PACKAGE_TARNAME “netcdf”
| #define PACKAGE_VERSION “3.6.3”
| #define PACKAGE_STRING “netCDF 3.6.3”
| #define PACKAGE_BUGREPORT “support@unidata.ucar.edu
| #define PACKAGE “netcdf”
| #define VERSION “3.6.3”
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE “.”
| /
end confdefs.h. */
|
| int
| main ()
| {
| #ifndef GNUC
| choke me
| #endif
|
| ;
| return 0;
| }

I get the feeling I am missing something in my library path but have no idea what.
Any ideas would be appreciated!


The netcdf config.log is included at the bottom.












This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by netCDF configure 3.6.3, which was
generated by GNU Autoconf 2.62. Invocation command line was

$ ./configure --prefix=/homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/tmp --disable-cxx

---------

Platform.

---------

hostname = mithras
uname -m = x86_64
uname -r = 2.6.9-55.ELsmp
uname -s = Linux
uname -v = #1 SMP Fri Apr 20 16:36:54 EDT 2007

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown

PATH: /scratch/cor/bin
PATH: /opt/vltmpi/OPENIB/mpi/bin
PATH: /usr/pgi/linux86-64/6.2/bin
PATH: /usr/local/sge/sge/bin/lx24-amd64
PATH: /usr/local/sge/bin/lx24-amd64
PATH: /usr/local/bin
PATH: /usr/X11R6/bin
PATH: /usr/bin
PATH: /bin

\

-----------

Core tests.

-----------

configure:2200: netCDF 3.6.3
configure:2241: checking build system type
configure:2259: result: x86_64-unknown-linux-gnu
configure:2281: checking host system type
configure:2296: result: x86_64-unknown-linux-gnu
configure:2343: checking for a BSD-compatible install
configure:2411: result: /usr/bin/install -c
configure:2422: checking whether build environment is sane
configure:2465: result: yes
configure:2490: checking for a thread-safe mkdir -p
configure:2529: result: /bin/mkdir -p
configure:2542: checking for gawk
configure:2558: found /usr/bin/gawk
configure:2569: result: gawk
configure:2580: checking whether make sets $(MAKE)
configure:2602: result: yes
configure:2794: checking user options
configure:2837: checking whether CXX is set to ‘’
configure:2841: result: no
configure:2845: checking whether FC is set to ‘’
configure:2849: result: no
configure:2853: checking whether F90 is set to ‘’
configure:2857: result: no
configure:2861: checking whether this is a netCDF-4.x build
configure:2869: result: no
configure:2961: checking whether netCDF extra tests should be run (developers only)
configure:2969: result: no
configure:2988: checking whether documentation is to be installed
configure:2996: result: no
configure:3008: checking whether Fortran compiler(s) should be tested during configure
configure:3016: result: yes
configure:3021: checking whether configure should try to set compiler flags
configure:3029: result: yes
configure:3033: checking whether FFIO will be used
configure:3041: result: no
configure:3054: checking whether to skip C++, F77, or F90 APIs if compiler is broken
configure:3062: result: yes
configure:3066: checking whether only the C library is desired
configure:3074: result: no
configure:3093: checking whether examples should be built
configure:3101: result: yes
configure:3105: checking whether F77 API is desired
configure:3114: result: yes
configure:3119: checking whether F90 API is desired
configure:3129: result: yes
configure:3133: checking whether fortran type sizes should be checked
configure:3141: result: yes
configure:3147: checking whether C API is desired
configure:3155: result: yes
configure:3162: checking where to get netCDF C-only library for separate fortran libraries
configure:3178: result:
configure:3193: checking whether CXX API is desired
configure:3202: result: no
configure:3213: checking whether v2 netCDF API should be built
configure:3221: result: yes
configure:3240: checking whether the ncgen/ncdump should be built
configure:3249: result: yes
configure:3261: checking whether large file (> 2GB) tests should be run
configure:3269: result: no
configure:3288: checking whether benchmaks should be run (experimental)
configure:3296: result: no
configure:3308: checking whether extreme numbers should be used in tests
configure:3323: result: yes
configure:3337: checking where to put large temp files if large file tests are run
configure:3346: result: .
configure:3357: checking whether a win32 DLL is desired
configure:3365: result: no
configure:3389: checking whether separate fortran libs are desired
configure:3398: result: no
configure:3468: finding C compiler
configure:3588: checking for C compiler version
configure:3596: /opt/vltmpi/OPENIB/mpi//bin/mpicc --version >&5
pgcc-Warning-Unknown switch: --version
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’
configure:3600: $? = 2
configure:3607: /opt/vltmpi/OPENIB/mpi//bin/mpicc -v >&5
mpicc for 1.2.6 (release) of : 2004/09/20 12:35:29

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -lmpich -lmpichfstub -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’
pgcc-Fatal-linker completed with exit code 1

configure:3611: $? = 2
configure:3618: /opt/vltmpi/OPENIB/mpi//bin/mpicc -V >&5
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’

pgcc 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:3622: $? = 2
configure:3645: checking for C compiler default output file name
configure:3667: /opt/vltmpi/OPENIB/mpi//bin/mpicc -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:3671: $? = 0
configure:3709: result: a.out
configure:3726: checking whether the C compiler works
configure:3736: ./a.out
configure:3740: $? = 0
configure:3757: result: yes
configure:3764: checking whether we are cross compiling
configure:3766: result: no
configure:3769: checking for suffix of executables
configure:3776: /opt/vltmpi/OPENIB/mpi//bin/mpicc -o conftest -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:3780: $? = 0
configure:3804: result:
configure:3810: checking for suffix of object files
configure:3836: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:3840: $? = 0
configure:3863: result: o
configure:3867: checking whether we are using the GNU C compiler
configure:3896: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
PGC-S-0040-Illegal use of symbol, choke (conftest.c: 17)
PGC-W-0156-Type not specified, ‘int’ assumed (conftest.c: 17)
PGC/x86-64 Linux/x86-64 6.2-5: compilation completed with severe errors
configure:3903: $? = 2
configure: failed program was:
| /* confdefs.h. /
| #define PACKAGE_NAME “netCDF”
| #define PACKAGE_TARNAME “netcdf”
| #define PACKAGE_VERSION “3.6.3”
| #define PACKAGE_STRING “netCDF 3.6.3”
| #define PACKAGE_BUGREPORT “support@unidata.ucar.edu
| #define PACKAGE “netcdf”
| #define VERSION “3.6.3”
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE “.”
| /
end confdefs.h. */
|
| int
| main ()
| {
| #ifndef GNUC
| choke me
| #endif
|
| ;
| return 0;
| }
configure:3920: result: no
configure:3929: checking whether /opt/vltmpi/OPENIB/mpi//bin/mpicc accepts -g
configure:3959: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -DNDEBUG -DpgiFortran conftest.c >&5
configure:3966: $? = 0
configure:4067: result: yes
configure:4084: checking for /opt/vltmpi/OPENIB/mpi//bin/mpicc option to accept ISO C89
configure:4158: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
PGC-W-0261-no macro replacement within a character constant (conftest.c: 46)
PGC/x86-64 Linux/x86-64 6.2-5: compilation completed with warnings
configure:4165: $? = 0
configure:4188: result: none needed
configure:4217: checking for style of include used by make
configure:4245: result: GNU
configure:4270: checking dependency style of /opt/vltmpi/OPENIB/mpi//bin/mpicc
configure:4361: result: none
configure:4377: checking whether /opt/vltmpi/OPENIB/mpi//bin/mpicc and cc understand -c and -o together
configure:4412: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c conftest.c -o conftest2.o >&5
configure:4416: $? = 0
configure:4422: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c conftest.c -o conftest2.o >&5
configure:4426: $? = 0
configure:4437: cc -c conftest.c >&5
configure:4441: $? = 0
configure:4449: cc -c conftest.c -o conftest2.o >&5
configure:4453: $? = 0
configure:4459: cc -c conftest.c -o conftest2.o >&5
configure:4463: $? = 0
configure:4481: result: yes
configure:4508: checking for an ANSI C-conforming const
configure:4583: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:4590: $? = 0
configure:4605: result: yes
configure:4636: finding Fortran compiler (will not be used if Fortran API is not desired)
configure:5032: checking for Fortran compiler version
configure:5040: /opt/vltmpi/OPENIB/mpi//bin/mpif90 --version >&5
pgf90-Warning-Unknown switch: --version
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’
configure:5044: $? = 2
configure:5051: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -v >&5
mpif90 for 1.2.6 (release) of : 2004/09/20 12:35:29

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o /usr/pgi/linux86-64/6.2/libso/f90main.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -L/lib -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -lmpichf90 -lmpichfarg -lmpich -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’
pgf90-Fatal-linker completed with exit code 1

configure:5055: $? = 2
configure:5062: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -V >&5
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’

pgf90 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:5066: $? = 2
configure:5074: checking whether we are using the GNU Fortran compiler
configure:5093: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.F >&5
conftest.F:
PGF90-S-0034-Syntax error at or near end of line (conftest.F: 3)
0 inform, 0 warnings, 1 severes, 0 fatal for main
configure:5100: $? = 2
configure: failed program was:
| program main
| #ifndef GNUC
| choke me
| #endif
|
| end
configure:5117: result: no
configure:5123: checking whether /opt/vltmpi/OPENIB/mpi//bin/mpif90 accepts -g
configure:5140: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g conftest.f >&5
conftest.f:
configure:5147: $? = 0
configure:5163: result: yes
configure:5313: checking for Fortran 77 compiler version
configure:5321: /opt/vltmpi/OPENIB/mpi//bin/mpif90 --version >&5
pgf90-Warning-Unknown switch: --version
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’
configure:5325: $? = 2
configure:5332: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -v >&5
mpif90 for 1.2.6 (release) of : 2004/09/20 12:35:29

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o /usr/pgi/linux86-64/6.2/libso/f90main.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -L/lib -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -lmpichf90 -lmpichfarg -lmpich -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’
pgf90-Fatal-linker completed with exit code 1

configure:5336: $? = 2
configure:5343: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -V >&5
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’

pgf90 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:5347: $? = 2
configure:5355: checking whether we are using the GNU Fortran 77 compiler
configure:5374: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.F >&5
conftest.F:
PGF90-S-0034-Syntax error at or near end of line (conftest.F: 3)
0 inform, 0 warnings, 1 severes, 0 fatal for main
configure:5381: $? = 2
configure: failed program was:
| program main
| #ifndef GNUC
| choke me
| #endif
|
| end
configure:5398: result: no
configure:5404: checking whether /opt/vltmpi/OPENIB/mpi//bin/mpif90 accepts -g
configure:5421: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g conftest.f >&5
conftest.f:
configure:5428: $? = 0
configure:5444: result: yes
configure:5492: setting up Fortran 90
configure:5511: checking for Fortran flag to compile .f90 files
configure:5533: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.f90 >&5
conftest.f90:
configure:5540: $? = 0
configure:5559: result: none
configure:5589: checking fortran 90 modules inclusion flag
configure:5620: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.f90 >&5
conftest.f90:
configure:5627: $? = 0
configure:5660: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 -Itmpdir_0 conftest.f90 >&5
conftest.f90:
configure:5667: $? = 0
configure:5698: result: -I
configure:5710: checking if Fortran compiler can handle Fortran-90
configure:5718: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.f90
conftest.f90:
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to pmpi_wtime_’
configure:5721: $? = 2
configure:5735: result: no
configure:5738: WARNING: No F90 compiler found. F90 API will not be built.
configure:5744: finding C++ compiler (will not be used if C++ API is not desired)
configure:5869: checking for C++ compiler version
configure:5877: mpicxx --version >&5
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’

pgCC (aka pgcpp) 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:5881: $? = 2
configure:5888: mpicxx -v >&5
mpiCC for 1.2.6 (release) of : 2004/09/20 12:35:29

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -lpmpich++ -lmpich -lmpichfstub -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lstd -lC -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’
pgCC-Fatal-linker completed with exit code 1

configure:5892: $? = 2
configure:5899: mpicxx -V >&5
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’

pgCC (aka pgcpp) 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:5903: $? = 2
configure:5906: checking whether we are using the GNU C++ compiler
configure:5935: mpicxx -c -g -O3 -DNDEBUG -DpgiFortran conftest.cpp >&5
“conftest.cpp”, line 17: error: identifier “choke” is undefined
choke me
^

“conftest.cpp”, line 17: warning: variable “me” was declared but never
referenced
choke me
^

1 error detected in the compilation of “conftest.cpp”.
configure:5942: $? = 2
configure: failed program was:
| /* confdefs.h. /
| #define PACKAGE_NAME “netCDF”
| #define PACKAGE_TARNAME “netcdf”
| #define PACKAGE_VERSION “3.6.3”
| #define PACKAGE_STRING “netCDF 3.6.3”
| #define PACKAGE_BUGREPORT “support@unidata.ucar.edu
| #define PACKAGE “netcdf”
| #define VERSION “3.6.3”
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE “.”
| /
end confdefs.h. /
|
| int
| main ()
| {
| #ifndef GNUC
| choke me
| #endif
|
| ;
| return 0;
| }
configure:5959: result: no
configure:5968: checking whether mpicxx accepts -g
configure:5998: mpicxx -c -g -DNDEBUG -DpgiFortran conftest.cpp >&5
configure:6005: $? = 0
configure:6106: result: yes
configure:6131: checking dependency style of mpicxx
configure:6222: result: none
configure:6295: setting up libtool
configure:6323: checking for a sed that does not truncate output
configure:6389: result: /bin/sed
configure:6407: checking for grep that handles long lines and -e
configure:6467: result: /bin/grep
configure:6472: checking for egrep
configure:6536: result: /bin/grep -E
configure:6541: checking for fgrep
configure:6605: result: /bin/grep -F
configure:6673: checking for non-GNU ld
configure:6707: result: /usr/bin/ld
configure:6716: checking if the linker (/usr/bin/ld) is GNU ld
configure:6731: result: yes
configure:6743: checking for BSD- or MS-compatible name lister (nm)
configure:6792: result: /usr/bin/nm -B
configure:6914: checking the name lister (/usr/bin/nm -B) interface
configure:6921: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:6924: /usr/bin/nm -B “conftest.o”
configure:6927: output
U __pgdbg_stub
0000000000000000 D some_variable
configure:6934: result: BSD nm
configure:6937: checking whether ln -s works
configure:6941: result: yes
configure:6949: checking the maximum length of command line arguments
configure:7069: result: 98304
configure:7086: checking whether the shell understands some XSI constructs
configure:7094: result: yes
configure:7098: checking whether the shell understands “+=”
configure:7104: result: no
configure:7139: checking for /usr/bin/ld option to reload object files
configure:7146: result: -r
configure:7173: checking how to recognize dependent libraries
configure:7363: result: pass_all
configure:7423: checking for ar
configure:7439: found /usr/bin/ar
configure:7450: result: ar
configure:7532: checking for strip
configure:7548: found /usr/bin/strip
configure:7559: result: strip
configure:7635: checking for ranlib
configure:7651: found /usr/bin/ranlib
configure:7662: result: ranlib
configure:7756: checking command to parse /usr/bin/nm -B output from /opt/vltmpi/OPENIB/mpi//bin/mpicc object
configure:7874: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:7877: $? = 0
configure:7881: /usr/bin/nm -B conftest.o | sed -n -e 's/^.
[ ]([ABCDGIRSTW][ABCDGIRSTW])[ ][ ]([_A-Za-z][_A-Za-z0-9])$/\1 \2 \2/p’ > conftest.nm
configure:7884: $? = 0
configure:7938: /opt/vltmpi/OPENIB/mpi//bin/mpicc -o conftest -g -O3 -DNDEBUG -DpgiFortran conftest.c conftstm.o >&5
configure:7941: $? = 0
configure:7979: result: ok
configure:8074: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:8077: $? = 0
configure:8562: checking how to run the C preprocessor
configure:8680: result: /opt/vltmpi/OPENIB/mpi//bin/mpicc -E
configure:8709: /opt/vltmpi/OPENIB/mpi//bin/mpicc -E -DNDEBUG -DpgiFortran conftest.c
configure:8716: $? = 0
configure:8747: /opt/vltmpi/OPENIB/mpi//bin/mpicc -E -DNDEBUG -DpgiFortran conftest.c
PGC-F-0206-Can’t find include file ac_nonexistent.h (conftest.c: 12)
PGC/x86-64 Linux/x86-64 6.2-5: compilation aborted
configure:8754: $? = 2
configure: failed program was:
| /
confdefs.h. /
| #define PACKAGE_NAME “netCDF”
| #define PACKAGE_TARNAME “netcdf”
| #define PACKAGE_VERSION “3.6.3”
| #define PACKAGE_STRING “netCDF 3.6.3”
| #define PACKAGE_BUGREPORT “support@unidata.ucar.edu
| #define PACKAGE “netcdf”
| #define VERSION “3.6.3”
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE “.”
| /
end confdefs.h. */
| #include <ac_nonexistent.h>
configure:8792: checking for ANSI C header files
configure:8822: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:8829: $? = 0
configure:8928: /opt/vltmpi/OPENIB/mpi//bin/mpicc -o conftest -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:8932: $? = 0
configure:8938: ./conftest
configure:8942: $? = 0
configure:8960: result: yes
configure:8984: checking for sys/types.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:8984: checking for sys/stat.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:8984: checking for stdlib.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:8984: checking for string.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:8984: checking for memory.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:8984: checking for strings.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:8984: checking for inttypes.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:8984: checking for stdint.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:8984: checking for unistd.h
configure:9005: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9012: $? = 0
configure:9029: result: yes
configure:9046: checking for dlfcn.h
configure:9067: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:9074: $? = 0
configure:9091: result: yes
configure:9221: checking for C++ compiler version
configure:9229: mpicxx --version >&5
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’

pgCC (aka pgcpp) 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:9233: $? = 2
configure:9240: mpicxx -v >&5
mpiCC for 1.2.6 (release) of : 2004/09/20 12:35:29

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -lpmpich++ -lmpich -lmpichfstub -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lstd -lC -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’
pgCC-Fatal-linker completed with exit code 1

configure:9244: $? = 2
configure:9251: mpicxx -V >&5
/usr/lib64/crt1.o(.text+0x21): In function _start': : undefined reference to main’

pgCC (aka pgcpp) 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:9255: $? = 2
configure:9258: checking whether we are using the GNU C++ compiler
configure:9311: result: no
configure:9320: checking whether mpicxx accepts -g
configure:9458: result: yes
configure:9483: checking dependency style of mpicxx
configure:9574: result: none
configure:9597: checking how to run the C++ preprocessor
configure:9633: mpicxx -E -DNDEBUG -DpgiFortran conftest.cpp
configure:9640: $? = 0
configure:9671: mpicxx -E -DNDEBUG -DpgiFortran conftest.cpp
“conftest.cpp”, line 23: error: could not open source file “ac_nonexistent.h”
#include <ac_nonexistent.h>
^

1 error detected in the compilation of “conftest.cpp”.
configure:9678: $? = 2
configure: failed program was:
| /* confdefs.h. /
| #define PACKAGE_NAME “netCDF”
| #define PACKAGE_TARNAME “netcdf”
| #define PACKAGE_VERSION “3.6.3”
| #define PACKAGE_STRING “netCDF 3.6.3”
| #define PACKAGE_BUGREPORT “support@unidata.ucar.edu
| #define PACKAGE “netcdf”
| #define VERSION “3.6.3”
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE “.”
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| /
end confdefs.h. */
| #include <ac_nonexistent.h>
configure:9711: result: mpicxx -E
configure:9740: mpicxx -E -DNDEBUG -DpgiFortran conftest.cpp
configure:9747: $? = 0
configure:9778: mpicxx -E -DNDEBUG -DpgiFortran conftest.cpp
“conftest.cpp”, line 23: error: could not open source file “ac_nonexistent.h”
#include <ac_nonexistent.h>
^

1 error detected in the compilation of “conftest.cpp”.
configure:9785: $? = 2
configure: failed program was:
| /* confdefs.h. /
| #define PACKAGE_NAME “netCDF”
| #define PACKAGE_TARNAME “netcdf”
| #define PACKAGE_VERSION “3.6.3”
| #define PACKAGE_STRING “netCDF 3.6.3”
| #define PACKAGE_BUGREPORT “support@unidata.ucar.edu
| #define PACKAGE “netcdf”
| #define VERSION “3.6.3”
| #define USE_EXTREME_NUMBERS 1
| #define TEMP_LARGE “.”
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| /
end confdefs.h. */
| #include <ac_nonexistent.h>
configure:9936: checking for Fortran 77 compiler version
configure:9944: /opt/vltmpi/OPENIB/mpi//bin/mpif90 --version >&5
pgf90-Warning-Unknown switch: --version
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’
configure:9948: $? = 2
configure:9955: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -v >&5
mpif90 for 1.2.6 (release) of : 2004/09/20 12:35:29

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o /usr/pgi/linux86-64/6.2/libso/f90main.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -L/lib -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -lmpichf90 -lmpichfarg -lmpich -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’
pgf90-Fatal-linker completed with exit code 1

configure:9959: $? = 2
configure:9966: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -V >&5
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’

pgf90 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:9970: $? = 2
configure:9978: checking whether we are using the GNU Fortran 77 compiler
configure:10021: result: no
configure:10027: checking whether /opt/vltmpi/OPENIB/mpi//bin/mpif90 accepts -g
configure:10067: result: yes
configure:10214: checking for Fortran compiler version
configure:10222: /opt/vltmpi/OPENIB/mpi//bin/mpif90 --version >&5
pgf90-Warning-Unknown switch: --version
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’
configure:10226: $? = 2
configure:10233: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -v >&5
mpif90 for 1.2.6 (release) of : 2004/09/20 12:35:29

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o /usr/pgi/linux86-64/6.2/libso/f90main.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -L/lib -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -lmpichf90 -lmpichfarg -lmpich -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’
pgf90-Fatal-linker completed with exit code 1

configure:10237: $? = 2
configure:10244: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -V >&5
/usr/pgi/linux86-64/6.2/libso/f90main.o(.text+0x3c): In function main': : undefined reference to MAIN_’
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90.so: undefined reference to pmpi_wtime_’

pgf90 6.2-5 64-bit target on x86-64 Linux
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.
configure:10248: $? = 2
configure:10256: checking whether we are using the GNU Fortran compiler
configure:10299: result: no
configure:10305: checking whether /opt/vltmpi/OPENIB/mpi//bin/mpif90 accepts -g
configure:10345: result: yes
configure:10827: checking for objdir
configure:10842: result: .libs
configure:11189: checking for /opt/vltmpi/OPENIB/mpi//bin/mpicc option to produce PIC
configure:11446: result: -DPIC
configure:11458: checking if /opt/vltmpi/OPENIB/mpi//bin/mpicc PIC flag -DPIC works
configure:11476: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran -DPIC -DPIC conftest.c >&5
configure:11480: $? = 0
configure:11493: result: yes
configure:11517: checking if /opt/vltmpi/OPENIB/mpi//bin/mpicc static flag works
configure:11545: result: yes
configure:11560: checking if /opt/vltmpi/OPENIB/mpi//bin/mpicc supports -c -o file.o
configure:11581: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran -o out/conftest2.o conftest.c >&5
configure:11585: $? = 0
configure:11607: result: yes
configure:11615: checking if /opt/vltmpi/OPENIB/mpi//bin/mpicc supports -c -o file.o
configure:11662: result: yes
configure:11695: checking whether the /opt/vltmpi/OPENIB/mpi//bin/mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:12761: result: yes
configure:13000: checking dynamic linker characteristics
configure:13443: /opt/vltmpi/OPENIB/mpi//bin/mpicc -o conftest -g -O3 -DNDEBUG -DpgiFortran -rpath /foo conftest.c >&5
conftest.c:
configure:13450: $? = 0
configure:13683: result: GNU/Linux ld.so
configure:13785: checking how to hardcode library paths into programs
configure:13810: result: immediate
configure:14651: checking whether stripping libraries is possible
configure:14656: result: yes
configure:14691: checking if libtool supports shared libraries
configure:14693: result: yes
configure:14696: checking whether to build shared libraries
configure:14717: result: no
configure:14720: checking whether to build static libraries
configure:14724: result: yes
configure:15020: checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:15990: result: yes
configure:16018: mpicxx -c -g -O3 -DNDEBUG -DpgiFortran conftest.cpp >&5
configure:16021: $? = 0
configure:16203: checking for mpicxx option to produce PIC
configure:16512: result: -DPIC
configure:16521: checking if mpicxx PIC flag -DPIC works
configure:16539: mpicxx -c -g -O3 -DNDEBUG -DpgiFortran -DPIC -DPIC conftest.cpp >&5
configure:16543: $? = 0
configure:16556: result: yes
configure:16577: checking if mpicxx static flag works
configure:16605: result: yes
configure:16617: checking if mpicxx supports -c -o file.o
configure:16638: mpicxx -c -g -O3 -DNDEBUG -DpgiFortran -o out/conftest2.o conftest.cpp >&5
configure:16642: $? = 0
configure:16664: result: yes
configure:16669: checking if mpicxx supports -c -o file.o
configure:16716: result: yes
configure:16746: checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:16772: result: yes
configure:16909: checking dynamic linker characteristics
configure:17300: mpicxx -o conftest -g -O3 -DNDEBUG -DpgiFortran conftest.cpp >&5
configure:17307: $? = 0
configure:17540: result: GNU/Linux ld.so
configure:17591: checking how to hardcode library paths into programs
configure:17616: result: unsupported
configure:17757: checking if libtool supports shared libraries
configure:17759: result: yes
configure:17762: checking whether to build shared libraries
configure:17782: result: no
configure:17785: checking whether to build static libraries
configure:17789: result: yes
configure:17803: checking for /opt/vltmpi/OPENIB/mpi//bin/mpif90 option to produce PIC
configure:18060: result:
configure:18125: checking if /opt/vltmpi/OPENIB/mpi//bin/mpif90 static flag works
configure:18153: result: no
configure:18165: checking if /opt/vltmpi/OPENIB/mpi//bin/mpif90 supports -c -o file.o
configure:18186: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 -o out/conftest2.o conftest.f >&5
conftest.f:
configure:18190: $? = 0
configure:18212: result: yes
configure:18217: checking if /opt/vltmpi/OPENIB/mpi//bin/mpif90 supports -c -o file.o
configure:18264: result: yes
configure:18294: checking whether the /opt/vltmpi/OPENIB/mpi//bin/mpif90 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:19340: result: yes
configure:19477: checking dynamic linker characteristics
configure:19858: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -o conftest -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 -rpath /foo conftest.f >&5
conftest.f:
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to pmpi_wtime_’
configure:19865: $? = 2
configure: failed program was:
| program main
|
| end
configure:20098: result: GNU/Linux ld.so
configure:20149: checking how to hardcode library paths into programs
configure:20174: result: immediate
configure:20310: checking if libtool supports shared libraries
configure:20312: result: yes
configure:20315: checking whether to build shared libraries
configure:20335: result: no
configure:20338: checking whether to build static libraries
configure:20342: result: yes
configure:20368: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.f90 >&5
conftest.f90:
configure:20371: $? = 0
configure:20481: checking for /opt/vltmpi/OPENIB/mpi//bin/mpif90 option to produce PIC
configure:20738: result:
configure:20803: checking if /opt/vltmpi/OPENIB/mpi//bin/mpif90 static flag works
configure:20831: result: no
configure:20843: checking if /opt/vltmpi/OPENIB/mpi//bin/mpif90 supports -c -o file.o
configure:20864: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 -o out/conftest2.o conftest.f90 >&5
conftest.f90:
configure:20868: $? = 0
configure:20890: result: yes
configure:20895: checking if /opt/vltmpi/OPENIB/mpi//bin/mpif90 supports -c -o file.o
configure:20942: result: yes
configure:20972: checking whether the /opt/vltmpi/OPENIB/mpi//bin/mpif90 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:22018: result: yes
configure:22155: checking dynamic linker characteristics
configure:22536: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -o conftest -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 -rpath /foo conftest.f90 >&5
conftest.f90:
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to pmpi_wtime_’
configure:22543: $? = 2
configure: failed program was:
| program main
|
| end
configure:22776: result: GNU/Linux ld.so
configure:22827: checking how to hardcode library paths into programs
configure:22852: result: immediate
configure:22900: finding other utilities
configure:22917: checking for a BSD-compatible install
configure:22985: result: /usr/bin/install -c
configure:22998: trying to set fortran flags for this platform
configure:23051: trying to set flags for this platform
configure:23056: checking if _HPUX_SOURCE should be set
configure:23072: result: no
configure:23077: checking if Solaris -Xa option is needed
configure:23090: result: CFLAGS=-g -O3
configure:23116: checking if we need to set _LARGE_FILES despite results of previous tests
configure:23147: result: LARGE_FILES=
configure:23157: checking for special C compiler options needed for large files
configure:23197: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:23204: $? = 0
configure:23252: result: no
configure:23258: checking for FILE_OFFSET_BITS value needed for large files
configure:23293: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -g -O3 -DNDEBUG -DpgiFortran conftest.c >&5
configure:23300: $? = 0
configure:23369: result: no
configure:23507: displaying some results
configure:23513: checking CPPFLAGS
configure:23515: result: -DNDEBUG -DpgiFortran
configure:23517: checking CC CFLAGS
configure:23519: result: /opt/vltmpi/OPENIB/mpi//bin/mpicc -g -O3
configure:23522: checking type /opt/vltmpi/OPENIB/mpi//bin/mpicc
configure:23524: result: /opt/vltmpi/OPENIB/mpi//bin/mpicc is /opt/vltmpi/OPENIB/mpi//bin/mpicc
configure:23527: checking CXX
configure:23530: result: mpicxx
configure:23532: checking CXXFLAGS
configure:23534: result: -g -O3
configure:23537: checking type mpicxx
configure:23539: result: mpicxx is /opt/vltmpi/OPENIB/mpi/bin/mpicxx
configure:23546: checking FC
configure:23549: result: /opt/vltmpi/OPENIB/mpi//bin/mpif90
configure:23551: checking FFLAGS
configure:23553: result: -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2
configure:23556: checking type /opt/vltmpi/OPENIB/mpi//bin/mpif90
configure:23558: result: /opt/vltmpi/OPENIB/mpi//bin/mpif90 is /opt/vltmpi/OPENIB/mpi//bin/mpif90
configure:23565: checking F90
configure:23580: result: unset
configure:23584: checking AR
configure:23587: result: ar
configure:23589: checking AR_FLAGS
configure:23591: result: cru
configure:23594: checking type ar
configure:23596: result: ar is /usr/bin/ar
configure:23603: checking NM
configure:23606: result: /usr/bin/nm -B
configure:23608: checking NMFLAGS
configure:23610: result:
configure:23682: checking for /usr/bin/nm
configure:23709: result: /usr/bin/nm -B
configure:23722: checking nm flags
configure:23727: result:
configure:23739: checking for C-equivalent to Fortran routine “SUB”
configure:23746: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.f
conftest.f:
configure:23749: $? = 0
configure:23761: result: sub

configure:23783: checking for Fortran “byte”
configure:23791: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.f
conftest.f:
configure:23794: $? = 0
configure:23796: result: yes
configure:23814: checking for Fortran “integer*2”
configure:23822: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -c -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftest.f
conftest.f:
configure:23825: $? = 0
configure:23827: result: yes
configure:23854: checking if Fortran “byte” is C “signed char”
configure:23864: /opt/vltmpi/OPENIB/mpi//bin/mpicc -c -DNDEBUG -DpgiFortran -g -O3 conftest.c
configure:23867: $? = 0
configure:23870: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 -c conftestf.f
conftestf.f:
configure:23873: $? = 0
configure:23876: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -o conftest -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftestf.o conftest.o
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to pmpi_wtick_' /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to pmpi_wtime

configure:23879: $? = 2
configure:23902: error: Could not link conftestf.o and conftest.o

----------------

Cache variables.

----------------

ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_compiler_gnu=no
ac_cv_c_const=yes
ac_cv_cxx_compiler_gnu=no
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=/opt/vltmpi/OPENIB/mpi//bin/mpicc
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value=’-g -O3 ’
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=’-DNDEBUG -DpgiFortran’
ac_cv_env_CPP_set=set
ac_cv_env_CPP_value=’/opt/vltmpi/OPENIB/mpi//bin/mpicc -E’
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=set
ac_cv_env_CXXFLAGS_value=’-g -O3 ’
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=mpicxx
ac_cv_env_F77_set=set
ac_cv_env_F77_value=/opt/vltmpi/OPENIB/mpi//bin/mpif90
ac_cv_env_FCFLAGS_set=set
ac_cv_env_FCFLAGS_value=’ -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2’
ac_cv_env_FC_set=set
ac_cv_env_FC_value=/opt/vltmpi/OPENIB/mpi//bin/mpif90
ac_cv_env_FFLAGS_set=set
ac_cv_env_FFLAGS_value=’ -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2’
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_f77_compiler_gnu=no
ac_cv_fc_compiler_gnu=no
ac_cv_fc_srcext_f90=none
ac_cv_header_dlfcn_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_objext=o
ac_cv_path_EGREP=’/bin/grep -E’
ac_cv_path_FGREP=’/bin/grep -F’
ac_cv_path_GREP=/bin/grep
ac_cv_path_SED=/bin/sed
ac_cv_path_install=’/usr/bin/install -c’
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP=’/opt/vltmpi/OPENIB/mpi//bin/mpicc -E’
ac_cv_prog_CXXCPP=‘mpicxx -E’
ac_cv_prog_NM=’/usr/bin/nm -B’
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc__opt_vltmpi_OPENIB_mpi__bin_mpicc_c_o=yes
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_f77_g=yes
ac_cv_prog_f90_uppercase_mod=no
ac_cv_prog_fc_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_sys_file_offset_bits=no
ac_cv_sys_largefile_CC=no
am_cv_CC_dependencies_compiler_type=none
am_cv_CXX_dependencies_compiler_type=none
ax_cv_f90_modflag=-I
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd=’$MAGIC_CMD’
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface=‘BSD nm’
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/bin/ld
lt_cv_path_LDCXX=
lt_cv_path_NM=’/usr/bin/nm -B’
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
lt_cv_prog_compiler_c_o_F77=yes
lt_cv_prog_compiler_c_o_FC=yes
lt_cv_prog_compiler_pic_works=yes
lt_cv_prog_compiler_pic_works_CXX=yes
lt_cv_prog_compiler_static_works=yes
lt_cv_prog_compiler_static_works_CXX=yes
lt_cv_prog_compiler_static_works_F77=no
lt_cv_prog_compiler_static_works_FC=no
lt_cv_prog_gnu_ld=yes
lt_cv_prog_gnu_ldcxx=
lt_cv_sys_global_symbol_pipe=‘sed -n -e ‘’‘s/^.[ ]([ABCDGIRSTW][ABCDGIRSTW])[ ][ ]([_A-Za-z][_A-Za-z0-9])$/\1 \2 \2/p’’’’
lt_cv_sys_global_symbol_to_c_name_address=‘sed -n -e ‘’‘s/^: ([^ ]) $/ {"\1", (void ) 0},/p’’’ -e ‘’'s/^[ABCDGIRSTW] ([^ ]) ([^ ])$/ {"\2", (void ) &\2},/p’’’’
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e ‘’'s/^: ([^ ]
) $/ {"\1", (void ) 0},/p’’’ -e ‘’'s/^[ABCDGIRSTW] ([^ ]
) (lib[^ ])$/ {"\2", (void ) &\2},/p’’’ -e ‘’'s/^[ABCDGIRSTW] ([^ ]) ([^ ])$/ {“lib\2”, (void ) &\2},/p’’’’
lt_cv_sys_global_symbol_to_cdecl='sed -n -e ‘’'s/^T .
(.
)$/extern int \1();/p’’’ -e ‘’‘s/^[ABCDGIRSTW]* .* (.*)$/extern char \1;/p’’’’
lt_cv_sys_max_cmd_len=98304

-----------------

Output variables.

-----------------

ACLOCAL=’${SHELL} /homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/netcdf-3.6.3/missing --run aclocal-1.10’
ALLOCA=’’
AMDEPBACKSLASH=’’
AMDEP_FALSE=’#’
AMDEP_TRUE=’’
AMTAR=’${SHELL} /homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/netcdf-3.6.3/missing --run tar’
AR=‘ar’
AS=‘as’
AUTOCONF=’${SHELL} /homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/netcdf-3.6.3/missing --run autoconf’
AUTOHEADER=’${SHELL} /homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/netcdf-3.6.3/missing --run autoheader’
AUTOMAKE=’${SHELL} /homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/netcdf-3.6.3/missing --run automake-1.10’
AWK=‘gawk’
BINFILE_NAME=’’
BUILD_BENCHMARKS_FALSE=’’
BUILD_BENCHMARKS_TRUE=’#’
BUILD_CXX4_FALSE=’’
BUILD_CXX4_TRUE=’#’
BUILD_CXX_FALSE=’’
BUILD_CXX_TRUE=’#’
BUILD_C_FALSE=’#’
BUILD_C_TRUE=’’
BUILD_DAP_FALSE=’’
BUILD_DAP_TRUE=’#’
BUILD_DLL_FALSE=’’
BUILD_DLL_TRUE=’#’
BUILD_EXAMPLES_FALSE=’’
BUILD_EXAMPLES_TRUE=’’
BUILD_F77_FALSE=’#’
BUILD_F77_TRUE=’’
BUILD_F90_FALSE=’’
BUILD_F90_TRUE=’#’
BUILD_SEPARATE_FORTRAN_FALSE=’’
BUILD_SEPARATE_FORTRAN_TRUE=’#’
BUILD_SHARED_FALSE=’’
BUILD_SHARED_TRUE=’#’
BUILD_UTILITIES_FALSE=’#’
BUILD_UTILITIES_TRUE=’’
BUILD_V2_FALSE=’#’
BUILD_V2_TRUE=’’
CC=’/opt/vltmpi/OPENIB/mpi//bin/mpicc’
CCDEPMODE=‘depmode=none’
CFLAGS=’-g -O3 ’
CPP=’/opt/vltmpi/OPENIB/mpi//bin/mpicc -E’
CPPFLAGS=’-DNDEBUG -DpgiFortran’
CXX=‘mpicxx’
CXXCPP=‘mpicxx -E’
CXXDEPMODE=‘depmode=none’
CXXFLAGS=’-g -O3 ’
CYGPATH_W=‘echo’
DEFS=’’
DEPDIR=’.deps’
DLLTOOL=‘dlltool’
DSYMUTIL=’’
DUMPBIN=’’
ECHO_C=’’
ECHO_N=’-n’
ECHO_T=’’
EGREP=’/bin/grep -E’
EXEEXT=’’
EXTRA_EXAMPLE_TESTS_FALSE=’’
EXTRA_EXAMPLE_TESTS_TRUE=’#’
EXTRA_TESTS_FALSE=’’
EXTRA_TESTS_TRUE=’#’
F77=’/opt/vltmpi/OPENIB/mpi//bin/mpif90’
FC=’/opt/vltmpi/OPENIB/mpi//bin/mpif90’
FCFLAGS=’ -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2’
FCFLAGS_f90=’’
FFLAGS=’ -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2’
FGREP=’/bin/grep -F’
FTPBINDIR=’’
GREP=’/bin/grep’
INSTALL_DATA=’${INSTALL} -m 644’
INSTALL_DOCS_FALSE=’’
INSTALL_DOCS_TRUE=’#’
INSTALL_PROGRAM=’${INSTALL}’
INSTALL_SCRIPT=’${INSTALL}’
INSTALL_STRIP_PROGRAM=’$(install_sh) -c -s’
LARGE_FILE_TESTS_FALSE=’’
LARGE_FILE_TESTS_TRUE=’#’
LD=’/usr/bin/ld -m elf_x86_64’
LDFLAGS=’’
LEX=’’
LEXLIB=’’
LEX_OUTPUT_ROOT=’’
LIBOBJS=’’
LIBS=’’
LIBTOOL=’$(SHELL) $(top_builddir)/libtool’
LN_S=‘ln -s’
LTLIBOBJS=’’
MAKEINFO=’${SHELL} /homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/netcdf-3.6.3/missing --run makeinfo’
MAKEWHATIS_CMD=’’
MKDIR_P=’/bin/mkdir -p’
MOD_FLAG=’-I’
NETCDF_C_LIB=’’
NM=’/usr/bin/nm -B’
NMEDIT=’’
NMFLAGS=’’
OBJDUMP=‘objdump’
OBJEXT=‘o’
PACKAGE=‘netcdf’
PACKAGE_BUGREPORT=‘support@unidata.ucar.edu
PACKAGE_NAME=‘netCDF’
PACKAGE_STRING=‘netCDF 3.6.3’
PACKAGE_TARNAME=‘netcdf’
PACKAGE_VERSION=‘3.6.3’
PATH_SEPARATOR=’:’
RANLIB=‘ranlib’
SED=’/bin/sed’
SET_MAKE=’’
SHAREEXT=‘so’
SHELL=’/bin/sh’
STRIP=‘strip’
TEST_F77_FALSE=’#’
TEST_F77_TRUE=’’
TEST_PARALLEL_FALSE=’’
TEST_PARALLEL_TRUE=’’
UPPER_CASE_MOD_FALSE=’’
UPPER_CASE_MOD_TRUE=’’
USE_C99_TYPES_FALSE=’’
USE_C99_TYPES_TRUE=’’
USE_FFIO_FALSE=’’
USE_FFIO_TRUE=’#’
USE_HDF5_DIR_FALSE=’’
USE_HDF5_DIR_TRUE=’#’
USE_LOGGING_FALSE=’’
USE_LOGGING_TRUE=’#’
USE_NETCDF4_FALSE=’’
USE_NETCDF4_TRUE=’#’
USE_NETCDF_C_LIB_DIR_FALSE=’’
USE_NETCDF_C_LIB_DIR_TRUE=’#’
USE_RENAMEV3_FALSE=’’
USE_RENAMEV3_TRUE=’#’
USE_SZLIB_DIR_FALSE=’’
USE_SZLIB_DIR_TRUE=’#’
USE_ZLIB_DIR_FALSE=’’
USE_ZLIB_DIR_TRUE=’#’
VERSION=‘3.6.3’
WHATIS=’’
ac_ct_CC=’’
ac_ct_CXX=’’
ac_ct_DUMPBIN=’’
ac_ct_F77=’’
ac_ct_FC=’’
am__fastdepCC_FALSE=’’
am__fastdepCC_TRUE=’#’
am__fastdepCXX_FALSE=’’
am__fastdepCXX_TRUE=’#’
am__include=‘include’
am__isrc=’’
am__leading_dot=’.’
am__quote=’’
am__tar=’${AMTAR} chof - “$$tardir”’
am__untar=’${AMTAR} xf -’
bindir=’${exec_prefix}/bin’
build=‘x86_64-unknown-linux-gnu’
build_alias=’’
build_cpu=‘x86_64’
build_os=‘linux-gnu’
build_vendor=‘unknown’
datadir=’${datarootdir}’
datarootdir=’${prefix}/share’
docdir=’${datarootdir}/doc/${PACKAGE_TARNAME}’
dvidir=’${docdir}’
exec_prefix=‘NONE’
host=‘x86_64-unknown-linux-gnu’
host_alias=’’
host_cpu=‘x86_64’
host_os=‘linux-gnu’
host_vendor=‘unknown’
htmldir=’${docdir}’
includedir=’${prefix}/include’
infodir=’${datarootdir}/info’
install_sh=’$(SHELL) /homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/netcdf-3.6.3/install-sh’
libdir=’${exec_prefix}/lib’
libexecdir=’${exec_prefix}/libexec’
localedir=’${datarootdir}/locale’
localstatedir=’${prefix}/var’
lt_ECHO=‘echo’
mandir=’${datarootdir}/man’
mkdir_p=’/bin/mkdir -p’
oldincludedir=’/usr/include’
pdfdir=’${docdir}’
prefix=’/homes/cor/bin/src/abinit-5.8.3/plugins/netcdf/tmp’
prog=’’
program_transform_name=‘s,x,x,’
psdir=’${docdir}’
sbindir=’${exec_prefix}/sbin’
sharedstatedir=’${prefix}/com’
sysconfdir=’${prefix}/etc’
target_alias=’’

-----------

confdefs.h.

-----------

#define PACKAGE_NAME “netCDF”
#define PACKAGE_TARNAME “netcdf”
#define PACKAGE_VERSION “3.6.3”
#define PACKAGE_STRING “netCDF 3.6.3”
#define PACKAGE_BUGREPORT “support@unidata.ucar.edu
#define PACKAGE “netcdf”
#define VERSION “3.6.3”
#define USE_EXTREME_NUMBERS 1
#define TEMP_LARGE “.”
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_DLFCN_H 1
#define LT_OBJDIR “.libs/”
#define NF_INT1_T byte
#define NF_INT2_T integer*2

configure: exit 1

Hi Connor2,

Most of the errors are normal since configure is checking if you’re using the GNU compilers. The real failure is:

configure:23876: /opt/vltmpi/OPENIB/mpi//bin/mpif90 -o conftest -g -module /homes/cor/bin/src/abinit-5.8.3/tmp-modules -I/homes/cor/bin/src/abinit-5.8.3/tmp-modules -Mextend -O2 conftestf.o conftest.o
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to `pmpi_wtick_'
/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libmpichf90nc.so: undefined reference to `pmpi_wtime_'
configure:23879: $? = 2
configure:23902: error: Could not link conftestf.o and conftest.o

For some reason the symbols “pmpi_wtick_” and “pmpi_wtime_” can not be found. They should be defined the the “libmpich” library.

Try compiling (-c) the sample program below. Then link the resulting object using the verbose (-v) flag and post the output.

Also, please run the following command on your MPI installation’s mpich library and post the output.

nm /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libpmpich.so | grep wtime



% /opt/vltmpi/OPENIB/mpi/bin/mpif90 -c fpi.f
% /opt/vltmpi/OPENIB/mpi/bin/mpif90 -v fpi.o
% cat fpi.f
c**********************************************************************
c   pi.f - compute pi by integrating f(x) = 4/(1 + x**2)     
c     
c   Each node: 
c    1) receives the number of rectangles used in the approximation.
c    2) calculates the areas of it's rectangles.
c    3) Synchronizes for a global summation.
c   Node 0 prints the result.
c
c  Variables:
c
c    pi  the calculated result
c    n   number of points of integration.  
c    x           midpoint of each rectangle's interval
c    f           function to integrate
c    sum,pi      area of rectangles
c    tmp         temporary scratch space for global summation
c    i           do loop index
c****************************************************************************
      program main

      include 'mpif.h'

      double precision  PI25DT
      parameter        (PI25DT = 3.141592653589793238462643d0)

      double precision  mypi, pi, h, sum, x, f, a
      integer n, myid, numprocs, i, rc
c                                 function to integrate
      f(a) = 4.d0 / (1.d0 + a*a)

      call MPI_INIT( ierr )
      call MPI_COMM_RANK( MPI_COMM_WORLD, myid, ierr )
      call MPI_COMM_SIZE( MPI_COMM_WORLD, numprocs, ierr )
      print *, "Process ", myid, " of ", numprocs, " is alive"

      sizetype   = 1
      sumtype    = 2
      
 10   if ( myid .eq. 0 ) then
         write(6,98)
 98      format('Enter the number of intervals: (0 quits)')
         read(5,99) n
 99      format(i10)
      endif
      
      call MPI_BCAST(n,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)

c                                 check for quit signal
      if ( n .le. 0 ) goto 30

c                                 calculate the interval size
      h = 1.0d0/n

      sum  = 0.0d0
      do 20 i = myid+1, n, numprocs
         x = h * (dble(i) - 0.5d0)
         sum = sum + f(x)
 20   continue
      mypi = h * sum

c                                 collect all the partial sums
      call MPI_REDUCE(mypi,pi,1,MPI_DOUBLE_PRECISION,MPI_SUM,0,
     $     MPI_COMM_WORLD,ierr)

c                                 node 0 prints the answer.
      if (myid .eq. 0) then
         write(6, 97) pi, abs(pi - PI25DT)
 97      format('  pi is approximately: ', F18.16,
     +          '  Error is: ', F18.16)
      endif

      goto 10

 30   call MPI_FINALIZE(rc)
      stop
      end

Hi,

Thanks for the help!

The output of
$ nm /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libpmpich.so | grep wtime is:


00000000000a2730 W mpi_wtime
00000000000a2730 W mpi_wtime_
00000000000a2730 W mpi_wtime__
00000000000a2730 T pmpi_wtime
00000000000a273b t __pmpi_wtimeEND

and on compiling and linking the code I get:

mithras [x86_64] 1006$ /opt/vltmpi/OPENIB/mpi/bin/mpif90 -c pi.f
pi.f:
mithras [x86_64] 1008$ /opt/vltmpi/OPENIB/mpi/bin/mpif90 -v pi.o
mpif90 for 1.2.6 (release) of : 2004/09/20 12:35:29 

/usr/bin/ld /usr/lib64/crt1.o /usr/lib64/crti.o /usr/pgi/linux86-64/6.2/libso/trace_init.o /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtbegin.o /usr/pgi/linux86-64/6.2/libso/f90main.o -m elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2 /usr/pgi/linux86-64/6.2/lib/pgi.ld -L/lib -rpath-link /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -L/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib pi.o -lmpichf90 -lmpichfarg -lmpich -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib -R/opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared -R/usr/lib64 -L/usr/lib64 -libverbs -lpthread -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/libso -L/usr/pgi/linux86-64/6.2/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -rpath /usr/pgi/linux86-64/6.2/libso -rpath /usr/pgi/linux86-64/6.2/lib -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lm -lgcc -lc -lgcc /usr/lib/gcc/x86_64-redhat-linux/3.4.6//crtend.o /usr/lib64/crtn.o

it linked and produced an executable. Also doing a grep for wtick gives

mithras [x86_64] 1017$ nm /opt/vltmpi/OPENIB/mpi.pgcc.rsh/lib/shared/libpmpich.so | grep wtick
00000000000a2660 W mpi_wtick
00000000000a2660 W mpi_wtick_
00000000000a2660 W mpi_wtick__
00000000000a2660 T pmpi_wtick
00000000000a266b t __pmpi_wtickEND

Is the lack of a trailing underscore a problem?

Thanks again

Is the lack of a trailing underscore a problem?

Yes. You’ll need to go back and rebuild your MPI library so that it has Fortran interfaces. We have guide on building MPICH2 HERE. I would assume the same process would work for OpenIB but I have not tried it myself.

  • Mat

I was hoping that wouldn’t be the case, as I don’t have admin rights on the cluster.
I guess I can probably build the libraries in my local space though.

Anyway, thanks again for your help.