configure error of 6.10 with gfortran+openmpi on fedora

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Zhang Xiaole
Posts: 46
Joined: Thu Sep 15, 2011 7:13 am

configure error of 6.10 with gfortran+openmpi on fedora

Post by Zhang Xiaole » Sun Dec 04, 2011 4:00 pm

Hello dear users,
Recently,i was trying to complie abinit 6.10 with gfrotran and openmpi on my computer based on fedroa 15. But some errors come up when the i do the ./configure.
my harderware is intel i7 2600.
this is my config file

Code: Select all

prefix="/home/pariah"
enable_64bit_flags="yes"
enable_mpi="yes"
enable_mpi="yes"
with_mpi_prefix="/usr/lib64/openmpi"

when i type the command ./configure --with-config-file="fedora.ac"
it ending with an error.and this is my output file

Code: Select all

==============================================================================
 === Overall startup                                                        ===
 ==============================================================================

checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target 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 whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for gawk... (cached) gawk
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
configure: reading options from ./xiaole.ac

 ==============================================================================
 === Build-system information                                               ===
 ==============================================================================

configure: ABINIT version 6.10.1
configure: M4 010416 - Autoconf 026800 - Automake 011100 - Libtool 020204
configure: reporting user interface changes:
configure:  * new option --enable-gw-openmp is available

 ==============================================================================
 === Option consistency checking                                            ===
 ==============================================================================

configure: checking consistency of library-related options
configure:  |---> all OK
configure:
configure: checking consistency of plug-in options
configure:  |---> all OK
configure:
configure: checking consistency of experimental options
configure:  |---> all OK
configure:
configure:  |---> all OK
configure:
configure: parsing command-line options

 ==============================================================================
 === Connector startup                                                      ===
 ==============================================================================

configure: Initializing MPI support
configure: looking for MPI in /usr/lib64/openmpi
checking for a MPI C compiler... /usr/lib64/openmpi/bin/mpicc
checking for a MPI C++ compiler... /usr/lib64/openmpi/bin/mpicxx
checking for a MPI Fortran compiler... /usr/lib64/openmpi/bin/mpif90
checking for a MPI runner... /usr/lib64/openmpi/bin/mpirun
configure: GPU support disabled from command-line

 ==============================================================================
 === Utilities                                                              ===
 ==============================================================================

checking for sh... /bin/sh
checking for mv... /bin/mv
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for dvips... no
checking for dvipdf... dvipdf
checking for latex... no
checking for markdown... no
checking for patch... patch
checking for ps2pdf... ps2pdf
checking for tar... tar
checking for wget... wget
checking for curl... curl
configure: using internal version of MarkDown

 ==============================================================================
 === C support                                                              ===
 ==============================================================================

checking for gcc... /usr/lib64/openmpi/bin/mpicc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling...configure: error: in `/home/pariah/abinit-6.10.1':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

and this is my log file

Code: Select all

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

It was created by ABINIT configure 6.10.1, which was
generated by GNU Autoconf 2.68.  Invocation command line was

  $ ./configure --with-config-file=./xiaole.ac

## --------- ##
## Platform. ##
## --------- ##

hostname = Pariah
uname -m = x86_64
uname -r = 2.6.41.1-1.fc15.x86_64
uname -s = Linux
uname -v = #1 SMP Fri Nov 11 21:36:28 UTC 2011

/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: /usr/lib64/qt-3.3/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /sbin
PATH: /home/pariah/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:3622: checking build system type
configure:3636: result: x86_64-unknown-linux-gnu
configure:3656: checking host system type
configure:3669: result: x86_64-unknown-linux-gnu
configure:3689: checking target system type
configure:3702: result: x86_64-unknown-linux-gnu
configure:3744: checking for a BSD-compatible install
configure:3812: result: /usr/bin/install -c
configure:3823: checking whether build environment is sane
configure:3873: result: yes
configure:4014: checking for a thread-safe mkdir -p
configure:4053: result: /bin/mkdir -p
configure:4066: checking for gawk
configure:4082: found /usr/bin/gawk
configure:4093: result: gawk
configure:4104: checking whether make sets $(MAKE)
configure:4126: result: yes
configure:4568: checking whether make sets $(MAKE)
configure:4590: result: yes
configure:4600: checking whether ln -s works
configure:4604: result: yes
configure:4611: checking for a sed that does not truncate output
configure:4675: result: /bin/sed
configure:4684: checking for gawk
configure:4711: result: gawk
configure:4722: checking for grep that handles long lines and -e
configure:4780: result: /bin/grep
configure:4787: checking for egrep
configure:4849: result: /bin/grep -E
configure:5801: reading options from ./xiaole.ac
configure:7652: ABINIT version 6.10.1
configure:7662: M4 010416 - Autoconf 026800 - Automake 011100 - Libtool 020204
configure:7673: reporting user interface changes:
configure:7728:  * new option --enable-gw-openmp is available
configure:7965: checking consistency of library-related options
configure:8016:  |---> all OK
configure:8019:
configure:8028: checking consistency of plug-in options
configure:8041:  |---> all OK
configure:8044:
configure:8053: checking consistency of experimental options
configure:8068:  |---> all OK
configure:8071:
configure:8093:  |---> all OK
configure:8096:
configure:8105: parsing command-line options
configure:9199: Initializing MPI support
configure:9203: looking for MPI in /usr/lib64/openmpi
configure:9236: checking for a MPI C compiler
configure:9246: result: /usr/lib64/openmpi/bin/mpicc
configure:9250: checking for a MPI C++ compiler
configure:9263: result: /usr/lib64/openmpi/bin/mpicxx
configure:9267: checking for a MPI Fortran compiler
configure:9277: result: /usr/lib64/openmpi/bin/mpif90
configure:9281: checking for a MPI runner
configure:9297: result: /usr/lib64/openmpi/bin/mpirun
configure:9647: GPU support disabled from command-line
configure:9685: checking for sh
configure:9703: found /bin/sh
configure:9716: result: /bin/sh
configure:9726: checking for mv
configure:9744: found /bin/mv
configure:9757: result: /bin/mv
configure:9767: checking for perl
configure:9785: found /usr/bin/perl
configure:9798: result: /usr/bin/perl
configure:9808: checking for rm
configure:9826: found /bin/rm
configure:9839: result: /bin/rm
configure:9852: checking for dvips
configure:9882: result: no
configure:9894: checking for dvipdf
configure:9910: found /usr/bin/dvipdf
configure:9921: result: dvipdf
configure:9936: checking for latex
configure:9966: result: no
configure:9978: checking for markdown
configure:10008: result: no
configure:10020: checking for patch
configure:10036: found /usr/bin/patch
configure:10047: result: patch
configure:10062: checking for ps2pdf
configure:10078: found /usr/bin/ps2pdf
configure:10089: result: ps2pdf
configure:10104: checking for tar
configure:10120: found /bin/tar
configure:10131: result: tar
configure:10146: checking for wget
configure:10162: found /usr/bin/wget
configure:10173: result: wget
configure:10188: checking for curl
configure:10204: found /usr/bin/curl
configure:10215: result: curl
configure:10229: using internal version of MarkDown
configure:10578: checking for gcc
configure:10605: result: /usr/lib64/openmpi/bin/mpicc
configure:10834: checking for C compiler version
configure:10843: /usr/lib64/openmpi/bin/mpicc --version >&5
gcc (GCC) 4.6.1 20110908 (Red Hat 4.6.1-9)
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:10854: $? = 0
configure:10843: /usr/lib64/openmpi/bin/mpicc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.6.1/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.6.1 20110908 (Red Hat 4.6.1-9) (GCC)
configure:10854: $? = 0
configure:10843: /usr/lib64/openmpi/bin/mpicc -V >&5
gcc: error: unrecognized option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:10854: $? = 4
configure:10843: /usr/lib64/openmpi/bin/mpicc -qversion >&5
gcc: error: unrecognized option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:10854: $? = 4
configure:10874: checking whether the C compiler works
configure:10896: /usr/lib64/openmpi/bin/mpicc    conftest.c  >&5
configure:10900: $? = 0
configure:10948: result: yes
configure:10951: checking for C compiler default output file name
configure:10953: result: a.out
configure:10959: checking for suffix of executables
configure:10966: /usr/lib64/openmpi/bin/mpicc -o conftest    conftest.c  >&5
configure:10970: $? = 0
configure:10992: result:
configure:11014: checking whether we are cross compiling
configure:11022: /usr/lib64/openmpi/bin/mpicc -o conftest    conftest.c  >&5
configure:11026: $? = 0
configure:11033: ./conftest
./conftest: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
configure:11037: $? = 127
configure:11044: error: in `/home/pariah/abinit-6.10.1':
configure:11046: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=x86_64-unknown-linux-gnu
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## ----------------- ##
## Output variables. ##
## ----------------- ##

ABINIT_BINARY_PACKAGE=''
ABINIT_TARGET=''
ABINIT_VERSION='6.10.1'
ABINIT_VERSION_BASE='6.10'
ABINIT_VERSION_BUILD='20111203'
ABINIT_VERSION_MAJOR='6'
ABINIT_VERSION_MICRO='1'
ABINIT_VERSION_MINOR='10'
ABI_CPPFLAGS=''
ACLOCAL='${SHELL} /home/pariah/abinit-6.10.1/config/gnu/missing --run aclocal-1.11'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE=''
AMTAR='${SHELL} /home/pariah/abinit-6.10.1/config/gnu/missing --run tar'
AR=''
ARFLAGS=''
ARFLAGS_64BITS=''
ARFLAGS_CMD='rc'
ARFLAGS_DEBUG=''
ARFLAGS_EXTRA=''
ARFLAGS_HINTS=''
ARFLAGS_OPTIM=''
ATOMPAW_BIN=''
AUTOCONF='${SHELL} /home/pariah/abinit-6.10.1/config/gnu/missing --run autoconf'
AUTOHEADER='${SHELL} /home/pariah/abinit-6.10.1/config/gnu/missing --run autoheader'
AUTOMAKE='${SHELL} /home/pariah/abinit-6.10.1/config/gnu/missing --run automake-1.11'
AWK='gawk'
BAZAAR=''
BOURNE_SHELL='/bin/sh'
CC='/usr/lib64/openmpi/bin/mpicc'
CCDEPMODE=''
CC_LDFLAGS=''
CC_LDFLAGS_64BITS=''
CC_LDFLAGS_DEBUG=''
CC_LDFLAGS_EXTRA=''
CC_LDFLAGS_GPU=''
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CC_LDFLAGS_OPTIM=''
CC_LIBS=''
CC_LIBS_64BITS=''
CC_LIBS_DEBUG=''
CC_LIBS_EXTRA=''
CC_LIBS_GPU=''
CC_LIBS_HINTS=''
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CFLAGS_GPU=''
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CPP=''
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CXX='/usr/lib64/openmpi/bin/mpicxx'
CXXDEPMODE=''
CXXFLAGS=''
CXXFLAGS_64BITS=''
CXXFLAGS_ATOMPAW=''
CXXFLAGS_BIGDFT=''
CXXFLAGS_DEBUG=''
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CXXFLAGS_FOX=''
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CXX_LIBS_DEBUG=''
CXX_LIBS_EXTRA=''
CXX_LIBS_GPU=''
CXX_LIBS_HINTS=''
CXX_LIBS_OPTIM=''
CYGPATH_W='echo'
DEFS=''
DEPDIR=''
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DO_BUILD_01_GSL_EXT_TRUE=''
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with_libxc_libs=''
with_linalg_flavor='netlib'
with_linalg_incs=''
with_linalg_libs=''
with_math_flavor='none'
with_math_incs=''
with_math_libs=''
with_mpi_incs=''
with_mpi_level=''
with_mpi_libs=''
with_mpi_prefix='/usr/lib64/openmpi'
with_netcdf_incs=''
with_netcdf_libs=''
with_test_timeout='0'
with_timer_flavor='abinit'
with_timer_incs=''
with_timer_libs=''
with_trio_flavor='netcdf+etsf_io'
with_wannier90_bins=''
with_wannier90_incs=''
with_wannier90_libs=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "ABINIT"
#define PACKAGE_TARNAME "abinit"
#define PACKAGE_VERSION "6.10.1"
#define PACKAGE_STRING "ABINIT 6.10.1"
#define PACKAGE_BUGREPORT "https://bugs.launchpad.net/abinit/"
#define PACKAGE_URL ""
#define PACKAGE "abinit"
#define VERSION "6.10.1"
#define ABINIT_VERSION "6.10.1"
#define ABINIT_VERSION_MAJOR "6"
#define ABINIT_VERSION_MINOR "10"
#define ABINIT_VERSION_MICRO "1"
#define ABINIT_VERSION_BUILD "20111203"
#define ABINIT_VERSION_BASE "6.10"
#define HAVE_OS_LINUX 1

configure: exit 1

please help me , thanks in andvance.
Best wishes!


Xiaole
Phd student
Phys Department
Shanghai JiaoTong university, Shanghai, China

User avatar
jbeuken
Posts: 365
Joined: Tue Aug 18, 2009 9:24 pm
Contact:

Re: configure error of 6.10 with gfortran+openmpi on fedroa

Post by jbeuken » Sun Dec 04, 2011 10:47 pm

Hi,

in the config.log, you see that the "libmpi.so.1" library is not found :
...
configure:11026: $? = 0
configure:11033: ./conftest
./conftest: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
configure:11037: $? = 127
...


initialize the env variable "LD_LIBRARY_PATH" :

Code: Select all

export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH


regards

jmb
------
Jean-Michel Beuken
Computer Scientist

Zhang Xiaole
Posts: 46
Joined: Thu Sep 15, 2011 7:13 am

Re: configure error of 6.10 with gfortran+openmpi on fedroa

Post by Zhang Xiaole » Fri Dec 09, 2011 1:54 pm

jbeuken wrote:Hi,

in the config.log, you see that the "libmpi.so.1" library is not found :
...
configure:11026: $? = 0
configure:11033: ./conftest
./conftest: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory
configure:11037: $? = 127
...


initialize the env variable "LD_LIBRARY_PATH" :

Code: Select all

export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH


regards

jmb

Hi jmb
according to your advice, i can ran my compiling process completely, then i type make mj4 and make install.
all the binary programmes generated.But when i test the code , there are someting wrong both in sequence and paralle ran. more specifically,when i type the code

Code: Select all

../../../bin/abinit <tparal_1.files 

it end like this

Code: Select all

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 14.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

when i type the code

Code: Select all

 mpirun -np 2 ../../../bin/abinit <tparal_1.files

it end like this

Code: Select all

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 14.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 3563 on
node Pariah exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).


is there someting i miss?please guide me.
Phd student
Phys Department
Shanghai JiaoTong university, Shanghai, China

david.waroquiers
Posts: 138
Joined: Sat Aug 15, 2009 12:45 am

Re: configure error of 6.10 with gfortran+openmpi on fedroa

Post by david.waroquiers » Fri Dec 09, 2011 4:42 pm

Hello,

You still need the MPI libraries, did you export LD_LIBRARY_PATH when doing your calculations ?
You can add this line in your .bashrc file :
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH

It might solve your problem

David

Zhang Xiaole
Posts: 46
Joined: Thu Sep 15, 2011 7:13 am

Re: configure error of 6.10 with gfortran+openmpi on fedroa

Post by Zhang Xiaole » Mon Dec 12, 2011 5:55 pm

david.waroquiers wrote:Hello,

You still need the MPI libraries, did you export LD_LIBRARY_PATH when doing your calculations ?
You can add this line in your .bashrc file :
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH

It might solve your problem

David

Hi, David
Thank you for your advice. i have already exported LD_LIBRARY_PATH,but the problem is still. Then i look back to my log file of make, i found there were some Warnings that may be fatal to my compile,so i just picked them up like follow.

Code: Select all

libtool: compile:  /usr/lib64/openmpi/bin/mpif90 -I../libsrc -I. -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c netcdf.f90 -o netcdf.o
netcdf_text_variables.f90:60.93:
    Included at netcdf.f90:52:

numDims  ) = (/ 1, (product(localCount(:counter)), counter = 1, numDims - 1) /)
                                                                           1                 
Warning: DO loop at (1) will be executed zero times
/bin/sh ../libtool --tag=FC   --mode=link /usr/lib64/openmpi/bin/mpif90        -I../libsrc -I.  -ffree-form -g -ffree-line-length-none  -O2 -mtune=native -march=native -mfpmath=sse        -o libnetcdff90.la  typeSizes.lo  netcdf.lo 
libtool: link: ar cru .libs/libnetcdff90.a  typeSizes.o netcdf.o

Code: Select all

growshrink.f90:89.59:

  call comb_rot_grow_loc_1(nfl1,nfu1,nfl2,nfu2,nfl3,nfu3,x,w1,ibyz,ibzxx)
                                                           1
Warning: Dummy argument 'w1' with INTENT(IN) in variable definition context (actual argument to INTENT = OUT/INOUT) at (1)
growshrink.f90:93.60:

  call comb_rot_grow_loc_2(nfl1,nfu1,nfl2,nfu2,nfl3,nfu3,w1,w2,ibzxx,ibxxyy)
                                                            1
Warning: Dummy argument 'w2' with INTENT(IN) in variable definition context (actual argument to INTENT = OUT/INOUT) at (1)

Code: Select all

tail.f90:324.33:

          wfd%nseg_c,wfd%nvctr_c,wfd%keyg(1,1),wfd%keyv(1),&
                                 1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg_c' at (1)
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o restart.o  restart.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o geometry.o  geometry.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o davidson.o  davidson.f90
davidson.f90:150.7:

       psi(1+nvctrp*norbu),v,msg)
       1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'psi' at (1)
davidson.f90:296.10:

          psi(1+nvctrp*norbu),g,msg)
          1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'psi' at (1)
davidson.f90:352.43:

                                           psi(1+nvctrp*norbu),g,msg)
                                           1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'psi' at (1)
davidson.f90:537.10:

          psi(1+nvctrp*norbu),v,msg)
          1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'psi' at (1)
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o projectors.o  `test -f 'init/projectors.f90' || echo './'`init/projectors.f90
init/projectors.f90:214.19:

                   nlpspd%nboxp_c(1,1,iat),nlpspd%nboxp_f(1,1,iat),n1,n2,n3,&
                   1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'nboxp_c' at (1)
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o ionicpot.o  `test -f 'init/ionicpot.f90' || echo './'`init/ionicpot.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o gridmanipulation.o  `test -f 'init/gridmanipulation.f90' || echo './'`init/gridmanipulation.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o gauprod.o  `test -f 'init/gauprod.f90' || echo './'`init/gauprod.f90
init/gauprod.f90:845.38:

                       call gbasovrlp(A%xp(iexpo),A%psiat(iexpo),B%xp(jexpo),B%
                                      1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'expo1' at (1)
init/gauprod.f90:1422.66:

          rxyz(1),rxyz(2),rxyz(3),hx,hy,hz,wfd%nseg_c,wfd%nvctr_c,wfd%keyg(1,1)
                                                                  1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg_c' at (1)
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o denspotd.o  `test -f 'init/denspotd.f90' || echo './'`init/denspotd.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o logrid.o  `test -f 'init/logrid.f90' || echo './'`init/logrid.f90
init/logrid.f90:55.31:

  call make_ib_inv(logrid_big, ibxy_c,ibzzx_c,ibyyzz_c,0,n1,0,n2,0,n3)
                               1
Warning: Dummy argument 'ibxy_c' with INTENT(IN) in variable definition context (actual argument to INTENT = OUT/INOUT) at (1)
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o logrid_per.o  `test -f 'init/logrid_per.f90' || echo './'`init/logrid_per.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o inputguess.o  `test -f 'init/inputguess.f90' || echo './'`init/inputguess.f90
init/inputguess.f90:112.66:

        call iguess_generator(iproc,at%nzatom(ity),at%nelpsp(ity),at%psppar(0,0
                                                                  1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'psppar' at (1)
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o gautowav.o  `test -f 'init/gautowav.f90' || echo './'`init/gautowav.f90
init/gautowav.f90:476.19:

                   G%xp(iexpo),G%psiat(iexpo),&
                   1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'xp' at (1)
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o eleconf.o  `test -f 'init/eleconf.f90' || echo './'`init/eleconf.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o locreg.o  `test -f 'init/locreg.f90' || echo './'`init/locreg.f90
init/locreg.f90:215.41:

          Glr%wfd%nseg_c,Glr%wfd%nvctr_c,Glr%wfd%keyg(1,1),Glr%wfd%keyv(1),&
                                         1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:220.10:

          Glr%wfd%keyg(1,Glr%wfd%nseg_c+1),Glr%wfd%keyv(Glr%wfd%nseg_c+1),&
          1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:229.41:

          Glr%wfd%nseg_c,Glr%wfd%nvctr_c,Glr%wfd%keyg(1,1),Glr%wfd%keyv(1),&
                                         1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:235.10:

          Glr%wfd%keyg(1,Glr%wfd%nseg_c+1),Glr%wfd%keyv(Glr%wfd%nseg_c+1),&
          1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:502.38:

             wfdg%nseg_c,wfdg%nvctr_c,wfdg%keyg(1,1),wfdg%keyv(1),&
                                      1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:507.38:

             wfdg%nseg_f,wfdg%nvctr_f,wfdg%keyg(1,wfdg%nseg_c+1),wfdg%keyv(wfdg
                                      1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:523.32:

       wfdg%nseg_c,wfdg%nvctr_c,wfdg%keyg(1,1),wfdg%keyv(1),&
                                1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:528.32:

       wfdg%nseg_f,wfdg%nvctr_f,wfdg%keyg(1,wfdg%nseg_c+1),wfdg%keyv(wfdg%nseg_
                                1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:543.32:

       wfdg%nseg_c,wfdg%nvctr_c,wfdg%keyg(1,1),wfdg%keyv(1),&
                                1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
init/locreg.f90:548.32:

       wfdg%nseg_f,wfdg%nvctr_f,wfdg%keyg(1,wfdg%nseg_c+1),wfdg%keyv(wfdg%nseg_
                                1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'keyg' at (1)
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o precond.o  `test -f 'wfn_opt/precond.f90' || echo './'`wfn_opt/precond.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o orthogonality.o  `test -f 'wfn_opt/orthogonality.f90' || echo './'`wfn_opt/orthogonality.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o diis.o  `test -f 'wfn_opt/diis.f90' || echo './'`wfn_opt/diis.f90
/usr/lib64/openmpi/bin/mpif90 -I. -Imodules -I. -I..  -IPSolver -IPSolver/ABINIT-common -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c -o applyh.o  `test -f 'wfn_opt/applyh.f90' || echo './'`wfn_opt/applyh.f90
wfn_opt/applyh.f90:952.41:

                 call applyprojector(l,i,at%psppar(0,0,ityp),at%npspcode(ityp),&
                                         1
Warning: Element of assumed-shaped or pointer array passed to array dummy argument 'psppar' at (1)
Phd student
Phys Department
Shanghai JiaoTong university, Shanghai, China

Zhang Xiaole
Posts: 46
Joined: Thu Sep 15, 2011 7:13 am

Re: configure error of 6.10 with gfortran+openmpi on fedroa

Post by Zhang Xiaole » Wed Dec 14, 2011 3:35 pm

My promble has been sovled according to the solution of jmb
see viewtopic.php?f=2&t=1452
it seem like the version 1.5- openmpi dosnt work well with abinit
Thanks a lot
promlem sovled
Phd student
Phys Department
Shanghai JiaoTong university, Shanghai, China

User avatar
jbeuken
Posts: 365
Joined: Tue Aug 18, 2009 9:24 pm
Contact:

Re: configure error of 6.10 with gfortran+openmpi on fedroa

Post by jbeuken » Thu Jan 26, 2012 5:40 pm

Dear Xiaole,

Zhang Xiaole wrote:My problem has been sovled according to the solution of jmb
see viewtopic.php?f=2&t=1452
it seem like the version 1.5- openmpi doesnt work well with abinit
promlem sovled


I finally understood why ABINIT does not work with the "native" fedora openmpi package ( 1.5.4 ) : problem with mpi_io
mpi_io is enabled by default in build system of ABINIT

then, we must use "--disable-mpi-io" in the configure command

regards

jmb
------
Jean-Michel Beuken
Computer Scientist

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