Installing neuron (nrn 7.1) with openmpi

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vgoudar
Posts: 19
Joined: Fri Dec 03, 2010 3:41 am

Installing neuron (nrn 7.1) with openmpi

Post by vgoudar » Wed Feb 09, 2011 9:45 pm

Hi,

Im unable to configure neuron on a cluster running openmpi. I face similar issues on my multicore server. The installation goes fine with mpich2 on the server. This is the command I used on the cluser running openmpi:

./configure --prefix=`pwd` --without-iv --with-paranrn --with-mpi

The output to screen is as follows:

Code: Select all

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-redhat-linux-gnu
checking host system type... x86_64-redhat-linux-gnu
checking for style of include used by make... GNU
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
Not trying to build rpms for your system (use --enable-rpm-rules to override) 
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for gawk... (cached) gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for flex... flex
checking for yywrap in -lfl... yes
checking lex output file root... lex.yy
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for egrep... grep -E
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... g77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g77 accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... yes
checking if g77 static flag -static works... yes
checking if g77 supports -c -o file.o... yes
checking whether the g77 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for mpicc... mpicc
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
configure: error: Cannot compile MPI program
The config.log looks like this:

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 nrn configure 7.1, which was
generated by GNU Autoconf 2.59.  Invocation command line was

  $ ./configure --prefix=/u/home/campus/vgoudar/neuron/nrnPara --without-iv --with-parnrn --with-mpi

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

hostname = n168
uname -m = x86_64
uname -r = 2.6.18-194.26.1.el5
uname -s = Linux
uname -v = #1 SMP Tue Nov 9 12:54:20 EST 2010

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

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

PATH: /u/local/mpi/openmpi/current/bin
PATH: /u/systems/SGE6.2u5/bin/lx26-amd64
PATH: /u/local/compilers/intel/11.1/073/bin/intel64/
PATH: /u/local/intel/11.1/openmpi/1.4.2/bin
PATH: /u/local/bin
PATH: /u/local/sbin
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /u/home/campus/vgoudar/bin


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

configure:1637: checking for a BSD-compatible install
configure:1692: result: /usr/bin/install -c
configure:1703: checking whether build environment is sane
configure:1746: result: yes
configure:1811: checking for gawk
configure:1827: found /bin/gawk
configure:1837: result: gawk
configure:1847: checking whether make sets $(MAKE)
configure:1867: result: yes
configure:2058: checking build system type
configure:2076: result: x86_64-redhat-linux-gnu
configure:2084: checking host system type
configure:2098: result: x86_64-redhat-linux-gnu
configure:2521: checking for style of include used by make
configure:2549: result: GNU
configure:2626: checking for g++
configure:2642: found /usr/bin/g++
configure:2652: result: g++
configure:2668: checking for C++ compiler version
configure:2671: g++ --version </dev/null >&5
g++ (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
Copyright (C) 2006 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:2674: $? = 0
configure:2676: g++ -v </dev/null >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)
configure:2679: $? = 0
configure:2681: g++ -V </dev/null >&5
g++: '-V' option must have argument
configure:2684: $? = 1
configure:2707: checking for C++ compiler default output file name
configure:2710: g++    conftest.cc  >&5
configure:2713: $? = 0
configure:2759: result: a.out
configure:2764: checking whether the C++ compiler works
configure:2770: ./a.out
configure:2773: $? = 0
configure:2790: result: yes
configure:2797: checking whether we are cross compiling
configure:2799: result: no
configure:2802: checking for suffix of executables
configure:2804: g++ -o conftest    conftest.cc  >&5
configure:2807: $? = 0
configure:2832: result: 
configure:2838: checking for suffix of object files
configure:2859: g++ -c   conftest.cc >&5
configure:2862: $? = 0
configure:2884: result: o
configure:2888: checking whether we are using the GNU C++ compiler
configure:2912: g++ -c   conftest.cc >&5
configure:2918: $? = 0
configure:2922: test -z 
			 || test ! -s conftest.err
configure:2925: $? = 0
configure:2928: test -s conftest.o
configure:2931: $? = 0
configure:2944: result: yes
configure:2950: checking whether g++ accepts -g
configure:2971: g++ -c -g  conftest.cc >&5
configure:2977: $? = 0
configure:2981: test -z 
			 || test ! -s conftest.err
configure:2984: $? = 0
configure:2987: test -s conftest.o
configure:2990: $? = 0
configure:3001: result: yes
configure:3043: g++ -c -g -O2  conftest.cc >&5
configure:3049: $? = 0
configure:3053: test -z 
			 || test ! -s conftest.err
configure:3056: $? = 0
configure:3059: test -s conftest.o
configure:3062: $? = 0
configure:3088: g++ -c -g -O2  conftest.cc >&5
conftest.cc: In function 'int main()':
conftest.cc:16: error: 'exit' was not declared in this scope
configure:3094: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3043: g++ -c -g -O2  conftest.cc >&5
configure:3049: $? = 0
configure:3053: test -z 
			 || test ! -s conftest.err
configure:3056: $? = 0
configure:3059: test -s conftest.o
configure:3062: $? = 0
configure:3088: g++ -c -g -O2  conftest.cc >&5
configure:3094: $? = 0
configure:3098: test -z 
			 || test ! -s conftest.err
configure:3101: $? = 0
configure:3104: test -s conftest.o
configure:3107: $? = 0
configure:3132: checking dependency style of g++
configure:3222: result: gcc3
configure:3281: g++ -c -g -O2  conftest.cc >&5
configure:3287: $? = 0
configure:3291: test -z 
			 || test ! -s conftest.err
configure:3294: $? = 0
configure:3297: test -s conftest.o
configure:3300: $? = 0
configure:3707: checking for gcc
configure:3723: found /usr/bin/gcc
configure:3733: result: gcc
configure:3977: checking for C compiler version
configure:3980: gcc --version </dev/null >&5
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
Copyright (C) 2006 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:3983: $? = 0
configure:3985: gcc -v </dev/null >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)
configure:3988: $? = 0
configure:3990: gcc -V </dev/null >&5
gcc: '-V' option must have argument
configure:3993: $? = 1
configure:3996: checking whether we are using the GNU C compiler
configure:4020: gcc -c   conftest.c >&5
configure:4026: $? = 0
configure:4030: test -z 
			 || test ! -s conftest.err
configure:4033: $? = 0
configure:4036: test -s conftest.o
configure:4039: $? = 0
configure:4052: result: yes
configure:4058: checking whether gcc accepts -g
configure:4079: gcc -c -g  conftest.c >&5
configure:4085: $? = 0
configure:4089: test -z 
			 || test ! -s conftest.err
configure:4092: $? = 0
configure:4095: test -s conftest.o
configure:4098: $? = 0
configure:4109: result: yes
configure:4126: checking for gcc option to accept ANSI C
configure:4196: gcc  -c -g -O2  conftest.c >&5
configure:4202: $? = 0
configure:4206: test -z 
			 || test ! -s conftest.err
configure:4209: $? = 0
configure:4212: test -s conftest.o
configure:4215: $? = 0
configure:4233: result: none needed
configure:4251: gcc -c -g -O2  conftest.c >&5
conftest.c:2: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'me'
configure:4257: $? = 1
configure: failed program was:
| #ifndef __cplusplus
|   choke me
| #endif
configure:4392: checking dependency style of gcc
configure:4482: result: gcc3
configure:4504: checking how to run the C preprocessor
configure:4539: gcc -E  conftest.c
configure:4545: $? = 0
configure:4577: gcc -E  conftest.c
conftest.c:16:28: error: ac_nonexistent.h: No such file or directory
configure:4583: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:4622: result: gcc -E
configure:4646: gcc -E  conftest.c
configure:4652: $? = 0
configure:4684: gcc -E  conftest.c
conftest.c:16:28: error: ac_nonexistent.h: No such file or directory
configure:4690: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:4737: checking for gawk
configure:4763: result: gawk
configure:4786: checking for a BSD-compatible install
configure:4841: result: /usr/bin/install -c
configure:4857: checking for flex
configure:4873: found /usr/bin/flex
configure:4883: result: flex
configure:4896: checking for yywrap in -lfl
configure:4926: gcc -o conftest -g -O2   conftest.c -lfl   >&5
configure:4932: $? = 0
configure:4936: test -z 
			 || test ! -s conftest.err
configure:4939: $? = 0
configure:4942: test -s conftest
configure:4945: $? = 0
configure:4958: result: yes
configure:5036: checking lex output file root
configure:5047: flex conftest.l
configure:5050: $? = 0
configure:5062: result: lex.yy
configure:5067: checking whether yytext is a pointer
configure:5083: gcc -o conftest -g -O2   conftest.c  -lfl >&5
configure:5089: $? = 0
configure:5093: test -z 
			 || test ! -s conftest.err
configure:5096: $? = 0
configure:5099: test -s conftest
configure:5102: $? = 0
configure:5116: result: yes
configure:5134: checking for bison
configure:5150: found /usr/bin/bison
configure:5160: result: bison -y
configure:5171: checking whether ln -s works
configure:5175: result: yes
configure:5208: checking for a sed that does not truncate output
configure:5264: result: /bin/sed
configure:5267: checking for egrep
configure:5277: result: grep -E
configure:5293: checking for ld used by gcc
configure:5360: result: /usr/bin/ld
configure:5369: checking if the linker (/usr/bin/ld) is GNU ld
configure:5384: result: yes
configure:5389: checking for /usr/bin/ld option to reload object files
configure:5396: result: -r
configure:5414: checking for BSD-compatible nm
configure:5463: result: /usr/bin/nm -B
configure:5467: checking how to recognise dependent libraries
configure:5643: result: pass_all
configure:5730: gcc -c -g -O2  conftest.c >&5
configure:5733: $? = 0
configure:5875: checking for ANSI C header files
configure:5900: gcc -c -g -O2  conftest.c >&5
configure:5906: $? = 0
configure:5910: test -z 
			 || test ! -s conftest.err
configure:5913: $? = 0
configure:5916: test -s conftest.o
configure:5919: $? = 0
configure:6008: gcc -o conftest -g -O2   conftest.c  >&5
conftest.c: In function 'main':
conftest.c:34: warning: incompatible implicit declaration of built-in function 'exit'
configure:6011: $? = 0
configure:6013: ./conftest
configure:6016: $? = 0
configure:6031: result: yes
configure:6055: checking for sys/types.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6055: checking for sys/stat.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6055: checking for stdlib.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6055: checking for string.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6055: checking for memory.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6055: checking for strings.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6055: checking for inttypes.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6055: checking for stdint.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6055: checking for unistd.h
configure:6071: gcc -c -g -O2  conftest.c >&5
configure:6077: $? = 0
configure:6081: test -z 
			 || test ! -s conftest.err
configure:6084: $? = 0
configure:6087: test -s conftest.o
configure:6090: $? = 0
configure:6101: result: yes
configure:6127: checking dlfcn.h usability
configure:6139: gcc -c -g -O2  conftest.c >&5
configure:6145: $? = 0
configure:6149: test -z 
			 || test ! -s conftest.err
configure:6152: $? = 0
configure:6155: test -s conftest.o
configure:6158: $? = 0
configure:6168: result: yes
configure:6172: checking dlfcn.h presence
configure:6182: gcc -E  conftest.c
configure:6188: $? = 0
configure:6208: result: yes
configure:6243: checking for dlfcn.h
configure:6250: result: yes
configure:6273: checking how to run the C++ preprocessor
configure:6304: g++ -E  conftest.cc
configure:6310: $? = 0
configure:6342: g++ -E  conftest.cc
conftest.cc:28:28: error: ac_nonexistent.h: No such file or directory
configure:6348: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| #define YYTEXT_POINTER 1
| #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:6387: result: g++ -E
configure:6411: g++ -E  conftest.cc
configure:6417: $? = 0
configure:6449: g++ -E  conftest.cc
conftest.cc:28:28: error: ac_nonexistent.h: No such file or directory
configure:6455: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| #define YYTEXT_POINTER 1
| #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:6551: checking for g77
configure:6567: found /usr/bin/g77
configure:6577: result: g77
configure:6592: checking for Fortran 77 compiler version
configure:6595: g77 --version </dev/null >&5
GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-4)
Copyright (C) 2006 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
or type the command `info -f g77 Copying'.
configure:6598: $? = 0
configure:6600: g77 -v </dev/null >&5
Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,f77 --disable-libgcj --host=x86_64-redhat-linux
Thread model: posix
gcc version 3.4.6 20060404 (Red Hat 3.4.6-4)
configure:6603: $? = 0
configure:6605: g77 -V </dev/null >&5
g77: `-V' option must have argument
configure:6608: $? = 1
configure:6616: checking whether we are using the GNU Fortran 77 compiler
configure:6630: g77 -c  conftest.F >&5
configure:6636: $? = 0
configure:6640: test -z 
			 || test ! -s conftest.err
configure:6643: $? = 0
configure:6646: test -s conftest.o
configure:6649: $? = 0
configure:6662: result: yes
configure:6668: checking whether g77 accepts -g
configure:6680: g77 -c -g conftest.f >&5
configure:6686: $? = 0
configure:6690: test -z 
			 || test ! -s conftest.err
configure:6693: $? = 0
configure:6696: test -s conftest.o
configure:6699: $? = 0
configure:6711: result: yes
configure:6741: checking the maximum length of command line arguments
configure:6850: result: 32768
configure:6861: checking command to parse /usr/bin/nm -B output from gcc object
configure:6966: gcc -c -g -O2  conftest.c >&5
configure:6969: $? = 0
configure:6973: /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:6976: $? = 0
configure:7028: gcc -o conftest -g -O2   conftest.c conftstm.o >&5
configure:7031: $? = 0
configure:7069: result: ok
configure:7073: checking for objdir
configure:7088: result: .libs
configure:7178: checking for ar
configure:7194: found /usr/bin/ar
configure:7205: result: ar
configure:7258: checking for ranlib
configure:7274: found /usr/bin/ranlib
configure:7285: result: ranlib
configure:7338: checking for strip
configure:7354: found /usr/bin/strip
configure:7365: result: strip
configure:7637: checking if gcc supports -fno-rtti -fno-exceptions
configure:7655: gcc -c -g -O2  -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C
configure:7659: $? = 0
configure:7672: result: no
configure:7687: checking for gcc option to produce PIC
configure:7897: result: -fPIC
configure:7905: checking if gcc PIC flag -fPIC works
configure:7923: gcc -c -g -O2  -fPIC -DPIC conftest.c >&5
configure:7927: $? = 0
configure:7940: result: yes
configure:7968: checking if gcc static flag -static works
configure:7996: result: yes
configure:8006: checking if gcc supports -c -o file.o
configure:8027: gcc -c -g -O2  -o out/conftest2.o conftest.c >&5
configure:8031: $? = 0
configure:8053: result: yes
configure:8079: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:9037: result: yes
configure:9058: checking whether -lc should be explicitly linked in
configure:9063: gcc -c -g -O2  conftest.c >&5
configure:9066: $? = 0
configure:9081: gcc -shared conftest.o  -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| grep  -lc  \>/dev/null 2\>\&1
configure:9084: $? = 0
configure:9096: result: no
configure:9104: checking dynamic linker characteristics
configure:9497: gcc -c -g -O2  conftest.c >&5
configure:9500: $? = 0
configure:9713: result: GNU/Linux ld.so
configure:9722: checking how to hardcode library paths into programs
configure:9747: result: immediate
configure:9761: checking whether stripping libraries is possible
configure:9766: result: yes
configure:9892: checking for shl_load
configure:9949: gcc -o conftest -g -O2   conftest.c  >&5
/work/1274722.1.idre.q/ccJ9WGYg.o: In function `main':
/u/home/campus/vgoudar/neuron/nrnPara/conftest.c:67: undefined reference to `shl_load'
/work/1274722.1.idre.q/ccJ9WGYg.o:(.data+0x0): undefined reference to `shl_load'
collect2: ld returned 1 exit status
configure:9955: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| #define YYTEXT_POINTER 1
| #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.  */
| /* Define shl_load to an innocuous variant, in case <limits.h> declares shl_load.
|    For example, HP-UX 11i <limits.h> declares gettimeofday.  */
| #define shl_load innocuous_shl_load
| 
| /* System header to define __stub macros and hopefully few prototypes,
|     which can conflict with char shl_load (); below.
|     Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
|     <limits.h> exists even on freestanding compilers.  */
| 
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
| 
| #undef shl_load
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| {
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char shl_load ();
| /* The GNU C library defines this for functions which it implements
|     to always fail with ENOSYS.  Some functions are actually named
|     something starting with __ and the normal name is an alias.  */
| #if defined (__stub_shl_load) || defined (__stub___shl_load)
| choke me
| #else
| char (*f) () = shl_load;
| #endif
| #ifdef __cplusplus
| }
| #endif
| 
| int
| main ()
| {
| return f != shl_load;
|   ;
|   return 0;
| }
configure:9980: result: no
configure:9985: checking for shl_load in -ldld
configure:10015: gcc -o conftest -g -O2   conftest.c -ldld   >&5
/usr/bin/ld: cannot find -ldld
collect2: ld returned 1 exit status
configure:10021: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| #define YYTEXT_POINTER 1
| #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.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char shl_load ();
| int
| main ()
| {
| shl_load ();
|   ;
|   return 0;
| }
configure:10047: result: no
configure:10052: checking for dlopen
configure:10109: gcc -o conftest -g -O2   conftest.c  >&5
/work/1274722.1.idre.q/cciRrCFU.o: In function `main':
/u/home/campus/vgoudar/neuron/nrnPara/conftest.c:67: undefined reference to `dlopen'
/work/1274722.1.idre.q/cciRrCFU.o:(.data+0x0): undefined reference to `dlopen'
collect2: ld returned 1 exit status
configure:10115: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| #define YYTEXT_POINTER 1
| #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.  */
| /* Define dlopen to an innocuous variant, in case <limits.h> declares dlopen.
|    For example, HP-UX 11i <limits.h> declares gettimeofday.  */
| #define dlopen innocuous_dlopen
| 
| /* System header to define __stub macros and hopefully few prototypes,
|     which can conflict with char dlopen (); below.
|     Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
|     <limits.h> exists even on freestanding compilers.  */
| 
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
| 
| #undef dlopen
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| {
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char dlopen ();
| /* The GNU C library defines this for functions which it implements
|     to always fail with ENOSYS.  Some functions are actually named
|     something starting with __ and the normal name is an alias.  */
| #if defined (__stub_dlopen) || defined (__stub___dlopen)
| choke me
| #else
| char (*f) () = dlopen;
| #endif
| #ifdef __cplusplus
| }
| #endif
| 
| int
| main ()
| {
| return f != dlopen;
|   ;
|   return 0;
| }
configure:10140: result: no
configure:10145: checking for dlopen in -ldl
configure:10175: gcc -o conftest -g -O2   conftest.c -ldl   >&5
configure:10181: $? = 0
configure:10185: test -z 
			 || test ! -s conftest.err
configure:10188: $? = 0
configure:10191: test -s conftest
configure:10194: $? = 0
configure:10207: result: yes
configure:10382: checking whether a program can dlopen itself
configure:10456: gcc -o conftest -g -O2  -DHAVE_DLFCN_H  -Wl,--export-dynamic conftest.c -ldl  >&5
configure: In function 'main':
configure:10452: warning: incompatible implicit declaration of built-in function 'exit'
configure:10459: $? = 0
configure:10477: result: yes
configure:10482: checking whether a statically linked program can dlopen itself
configure:10556: gcc -o conftest -g -O2  -DHAVE_DLFCN_H  -Wl,--export-dynamic -static conftest.c -ldl  >&5
configure: In function 'main':
configure:10552: warning: incompatible implicit declaration of built-in function 'exit'
/work/1274722.1.idre.q/ccKLdwBg.o: In function `main':
/u/home/campus/vgoudar/neuron/nrnPara/configure:10540: warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
configure:10559: $? = 0
/u/local/intel/11.1/openmpi/1.4.2/lib/: cannot read file data: Is a directory
configure:10577: result: no
configure:10600: checking if libtool supports shared libraries
configure:10602: result: yes
configure:10605: checking whether to build shared libraries
configure:10626: result: yes
configure:10629: checking whether to build static libraries
configure:10633: result: no
configure:10725: creating libtool
configure:11316: checking for ld used by g++
configure:11383: result: /usr/bin/ld -m elf_x86_64
configure:11392: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
configure:11407: result: yes
configure:11458: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:12396: result: yes
configure:12414: g++ -c -g -O2  conftest.cpp >&5
configure:12417: $? = 0
configure:12536: checking for g++ option to produce PIC
configure:12810: result: -fPIC
configure:12818: checking if g++ PIC flag -fPIC works
configure:12836: g++ -c -g -O2  -fPIC -DPIC conftest.cpp >&5
configure:12840: $? = 0
configure:12853: result: yes
configure:12881: checking if g++ static flag -static works
configure:12909: result: yes
configure:12919: checking if g++ supports -c -o file.o
configure:12940: g++ -c -g -O2  -o out/conftest2.o conftest.cpp >&5
configure:12944: $? = 0
configure:12966: result: yes
configure:12992: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:13017: result: yes
configure:13084: checking dynamic linker characteristics
configure:13477: g++ -c -g -O2  conftest.cpp >&5
configure:13480: $? = 0
configure:13693: result: GNU/Linux ld.so
configure:13702: checking how to hardcode library paths into programs
configure:13727: result: immediate
configure:14256: checking if libtool supports shared libraries
configure:14258: result: yes
configure:14261: checking whether to build shared libraries
configure:14281: result: yes
configure:14284: checking whether to build static libraries
configure:14288: result: no
configure:14298: checking for g77 option to produce PIC
configure:14508: result: -fPIC
configure:14516: checking if g77 PIC flag -fPIC works
configure:14534: g77 -c -g -O2 -fPIC conftest.f >&5
configure:14538: $? = 0
configure:14551: result: yes
configure:14579: checking if g77 static flag -static works
configure:14607: result: yes
configure:14617: checking if g77 supports -c -o file.o
configure:14638: g77 -c -g -O2 -o out/conftest2.o conftest.f >&5
configure:14642: $? = 0
configure:14664: result: yes
configure:14690: checking whether the g77 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
configure:15628: result: yes
configure:15695: checking dynamic linker characteristics
configure:16088: g77 -c -g -O2 conftest.f >&5
configure:16091: $? = 0
configure:16304: result: GNU/Linux ld.so
configure:16313: checking how to hardcode library paths into programs
configure:16338: result: immediate
configure:20076: checking for cos in -lm
configure:20106: gcc -o conftest -g -O2   conftest.c -lm   >&5
conftest.c:35: warning: conflicting types for built-in function 'cos'
configure:20112: $? = 0
configure:20116: test -z 
			 || test ! -s conftest.err
configure:20119: $? = 0
configure:20122: test -s conftest
configure:20125: $? = 0
configure:20138: result: yes
configure:20651: checking for mpicc
configure:20667: found /u/local/mpi/openmpi/current/bin/mpicc
configure:20677: result: mpicc
configure:20694: checking for MPI_Init
configure:20751: mpicc -o conftest -g -O2   conftest.c  -lm >&5
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_endpoint.o): In function `mca_btl_openib_endpoint_destruct':
../../../../../ompi/mca/btl/openib/btl_openib_endpoint.c:(.text+0x807): undefined reference to `ibv_unreg_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_async.o): In function `btl_openib_async_thread':
../../../../../ompi/mca/btl/openib/btl_openib_async.c:(.text+0xd0d): undefined reference to `ibv_query_xrc_rcv_qp'
../../../../../ompi/mca/btl/openib/btl_openib_async.c:(.text+0xffc): undefined reference to `ibv_modify_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_async.o): In function `mca_btl_openib_load_apm_xrc_rcv':
../../../../../ompi/mca/btl/openib/btl_openib_async.c:(.text+0x16db): undefined reference to `ibv_query_xrc_rcv_qp'
../../../../../ompi/mca/btl/openib/btl_openib_async.c:(.text+0x1942): undefined reference to `ibv_modify_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_xrc.o): In function `mca_btl_openib_open_xrc_domain':
../../../../../ompi/mca/btl/openib/btl_openib_xrc.c:(.text+0x62): undefined reference to `ibv_open_xrc_domain'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_xrc.o): In function `mca_btl_openib_close_xrc_domain':
../../../../../ompi/mca/btl/openib/btl_openib_xrc.c:(.text+0x1d6): undefined reference to `ibv_close_xrc_domain'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_connect_xoob.o): In function `xoob_rml_recv_cb':
../../../../../ompi/mca/btl/openib/connect/btl_openib_connect_xoob.c:(.text+0xb8c): undefined reference to `ibv_reg_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_connect_xoob.o): In function `xoob_recv_qp_create':
../../../../../ompi/mca/btl/openib/connect/btl_openib_connect_xoob.c:(.text+0x191b): undefined reference to `ibv_create_xrc_rcv_qp'
../../../../../ompi/mca/btl/openib/connect/btl_openib_connect_xoob.c:(.text+0x1a0f): undefined reference to `ibv_modify_xrc_rcv_qp'
../../../../../ompi/mca/btl/openib/connect/btl_openib_connect_xoob.c:(.text+0x1b5d): undefined reference to `ibv_modify_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib.o): In function `mca_btl_openib_add_procs':
../../../../../ompi/mca/btl/openib/btl_openib.c:(.text+0x6c9): undefined reference to `ibv_create_xrc_srq'
configure:20757: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| #define YYTEXT_POINTER 1
| #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.  */
| /* Define MPI_Init to an innocuous variant, in case <limits.h> declares MPI_Init.
|    For example, HP-UX 11i <limits.h> declares gettimeofday.  */
| #define MPI_Init innocuous_MPI_Init
| 
| /* System header to define __stub macros and hopefully few prototypes,
|     which can conflict with char MPI_Init (); below.
|     Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
|     <limits.h> exists even on freestanding compilers.  */
| 
| #ifdef __STDC__
| # include <limits.h>
| #else
| # include <assert.h>
| #endif
| 
| #undef MPI_Init
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| {
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char MPI_Init ();
| /* The GNU C library defines this for functions which it implements
|     to always fail with ENOSYS.  Some functions are actually named
|     something starting with __ and the normal name is an alias.  */
| #if defined (__stub_MPI_Init) || defined (__stub___MPI_Init)
| choke me
| #else
| char (*f) () = MPI_Init;
| #endif
| #ifdef __cplusplus
| }
| #endif
| 
| int
| main ()
| {
| return f != MPI_Init;
|   ;
|   return 0;
| }
configure:20782: result: no
configure:20790: checking for MPI_Init in -lmpi
configure:20820: mpicc -o conftest -g -O2   conftest.c -lmpi   -lm >&5
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_endpoint.o): In function `mca_btl_openib_endpoint_destruct':
../../../../../ompi/mca/btl/openib/btl_openib_endpoint.c:(.text+0x807): undefined reference to `ibv_unreg_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_async.o): In function `btl_openib_async_thread':
../../../../../ompi/mca/btl/openib/btl_openib_async.c:(.text+0xd0d): undefined reference to `ibv_query_xrc_rcv_qp'
../../../../../ompi/mca/btl/openib/btl_openib_async.c:(.text+0xffc): undefined reference to `ibv_modify_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_async.o): In function `mca_btl_openib_load_apm_xrc_rcv':
../../../../../ompi/mca/btl/openib/btl_openib_async.c:(.text+0x16db): undefined reference to `ibv_query_xrc_rcv_qp'
../../../../../ompi/mca/btl/openib/btl_openib_async.c:(.text+0x1942): undefined reference to `ibv_modify_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_xrc.o): In function `mca_btl_openib_open_xrc_domain':
../../../../../ompi/mca/btl/openib/btl_openib_xrc.c:(.text+0x62): undefined reference to `ibv_open_xrc_domain'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_xrc.o): In function `mca_btl_openib_close_xrc_domain':
../../../../../ompi/mca/btl/openib/btl_openib_xrc.c:(.text+0x1d6): undefined reference to `ibv_close_xrc_domain'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_connect_xoob.o): In function `xoob_rml_recv_cb':
../../../../../ompi/mca/btl/openib/connect/btl_openib_connect_xoob.c:(.text+0xb8c): undefined reference to `ibv_reg_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_connect_xoob.o): In function `xoob_recv_qp_create':
../../../../../ompi/mca/btl/openib/connect/btl_openib_connect_xoob.c:(.text+0x191b): undefined reference to `ibv_create_xrc_rcv_qp'
../../../../../ompi/mca/btl/openib/connect/btl_openib_connect_xoob.c:(.text+0x1a0f): undefined reference to `ibv_modify_xrc_rcv_qp'
../../../../../ompi/mca/btl/openib/connect/btl_openib_connect_xoob.c:(.text+0x1b5d): undefined reference to `ibv_modify_xrc_rcv_qp'
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib.o): In function `mca_btl_openib_add_procs':
../../../../../ompi/mca/btl/openib/btl_openib.c:(.text+0x6c9): undefined reference to `ibv_create_xrc_srq'
configure:20826: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| #define YYTEXT_POINTER 1
| #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.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char MPI_Init ();
| int
| main ()
| {
| MPI_Init ();
|   ;
|   return 0;
| }
configure:20852: result: no
configure:20860: checking for MPI_Init in -lmpich
configure:20890: mpicc -o conftest -g -O2   conftest.c -lmpich   -lm >&5
ld: cannot find -lmpich
configure:20896: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME "nrn"
| #define PACKAGE_TARNAME "nrn"
| #define PACKAGE_VERSION "7.1"
| #define PACKAGE_STRING "nrn 7.1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "nrn"
| #define VERSION "7.1"
| #define DISCRETE_EVENT_OBSERVER 1
| #ifdef __cplusplus
| extern "C" void std::exit (int) throw (); using std::exit;
| #endif
| #define IVOS_DECLARE_TRUE
| #define YYTEXT_POINTER 1
| #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.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char MPI_Init ();
| int
| main ()
| {
| MPI_Init ();
|   ;
|   return 0;
| }
configure:20922: result: no
configure:20990: error: Cannot compile MPI program

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

ac_cv_build=x86_64-redhat-linux-gnu
ac_cv_build_alias=x86_64-redhat-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_F77_set=
ac_cv_env_F77_value=
ac_cv_env_FFLAGS_set=
ac_cv_env_FFLAGS_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_MPICC_set=
ac_cv_env_MPICC_value=
ac_cv_env_MPICXX_set=
ac_cv_env_MPICXX_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_exeext=
ac_cv_f77_compiler_gnu=yes
ac_cv_func_MPI_Init=no
ac_cv_func_dlopen=no
ac_cv_func_shl_load=no
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-redhat-linux-gnu
ac_cv_host_alias=x86_64-redhat-linux-gnu
ac_cv_lib_dl_dlopen=yes
ac_cv_lib_dld_shl_load=no
ac_cv_lib_fl_yywrap=yes
ac_cv_lib_m_cos=yes
ac_cv_lib_mpi_MPI_Init=no
ac_cv_lib_mpich_MPI_Init=no
ac_cv_objext=o
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_CXXCPP='g++ -E'
ac_cv_prog_LEX=flex
ac_cv_prog_MPICC=mpicc
ac_cv_prog_YACC='bison -y'
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_F77=g77
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_cxx_g=yes
ac_cv_prog_egrep='grep -E'
ac_cv_prog_f77_g=yes
ac_cv_prog_lex_root=lex.yy
ac_cv_prog_lex_yytext_pointer=yes
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
lt_cv_deplibs_check_method=pass_all
lt_cv_dlopen=dlopen
lt_cv_dlopen_libs=-ldl
lt_cv_dlopen_self=yes
lt_cv_dlopen_self_static=no
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/bin/ld
lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64'
lt_cv_path_NM='/usr/bin/nm -B'
lt_cv_path_SED=/bin/sed
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_rtti_exceptions=no
lt_cv_prog_gnu_ld=yes
lt_cv_prog_gnu_ldcxx=yes
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\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \([^ ]*\) \([^ ]*\)$/  {"\2", (lt_ptr) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^. .* \(.*\)$/extern int \1;/p'\'''
lt_cv_sys_max_cmd_len=32768
lt_lt_cv_prog_compiler_c_o='"yes"'
lt_lt_cv_prog_compiler_c_o_CXX='"yes"'
lt_lt_cv_prog_compiler_c_o_F77='"yes"'
lt_lt_cv_sys_global_symbol_pipe='"sed -n -e '\''s/^.*[ 	]\\([ABCDGIRSTW][ABCDGIRSTW]*\\)[ 	][ 	]*\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2 \\2/p'\''"'
lt_lt_cv_sys_global_symbol_to_c_name_address='"sed -n -e '\''s/^: \\([^ ]*\\) \$/  {\\\"\\1\\\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \\([^ ]*\\) \\([^ ]*\\)\$/  {\"\\2\", (lt_ptr) \\&\\2},/p'\''"'
lt_lt_cv_sys_global_symbol_to_cdecl='"sed -n -e '\''s/^. .* \\(.*\\)\$/extern int \\1;/p'\''"'

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /u/home/campus/vgoudar/neuron/nrnPara/missing --run aclocal-1.9'
ALLOCA=''
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /u/home/campus/vgoudar/neuron/nrnPara/missing --run tar'
AR='ar'
AUTOCONF='${SHELL} /u/home/campus/vgoudar/neuron/nrnPara/missing --run autoconf'
AUTOHEADER='${SHELL} /u/home/campus/vgoudar/neuron/nrnPara/missing --run autoheader'
AUTOMAKE='${SHELL} /u/home/campus/vgoudar/neuron/nrnPara/missing --run automake-1.9'
AWK='gawk'
BUILD_6229_FALSE=''
BUILD_6229_TRUE=''
BUILD_CARBON_FALSE=''
BUILD_CARBON_TRUE='#'
BUILD_CYGWIN_FALSE=''
BUILD_CYGWIN_TRUE=''
BUILD_IVOS_FALSE=''
BUILD_IVOS_TRUE=''
BUILD_MEMACS_FALSE=''
BUILD_MEMACS_TRUE=''
BUILD_NRNIV_FALSE=''
BUILD_NRNIV_TRUE=''
BUILD_NRNJAVA_FALSE=''
BUILD_NRNJAVA_TRUE=''
BUILD_NRNPYTHON_DYNAMIC_FALSE=''
BUILD_NRNPYTHON_DYNAMIC_TRUE=''
BUILD_NRNPYTHON_FALSE=''
BUILD_NRNPYTHON_TRUE=''
BUILD_PARANEURON_FALSE=''
BUILD_PARANEURON_TRUE=''
BUILD_READLINE_FALSE=''
BUILD_READLINE_TRUE=''
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
CXX='g++'
CXXCPP='g++ -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
ECHO='echo'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='grep -E'
EXEEXT=''
EXTRA_CYGWIN_FLAGS='$(EXTRA_CYGWIN)'
F77='g77'
FFLAGS='-g -O2'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
IVOS_DIR=''
IVOS_LIB=''
IV_INCLUDE=''
IV_LIBDIR=''
IV_LIBS=''
IV_LIBS_LIBTOOL=''
JAVA=''
JAVAC=''
JAVAH=''
JDKDIR=''
JNI_INCLUDE_FLAGS=''
LDFLAGS=''
LEX='flex'
LEXLIB='-lfl'
LEX_OUTPUT_ROOT='lex.yy'
LIBOBJS=''
LIBS=' -lm'
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIBTOOLTAG=''
LN_S='ln -s'
LTLIBOBJS=''
MAC_DARWIN_FALSE=''
MAC_DARWIN_TRUE=''
MAKEINFO='${SHELL} /u/home/campus/vgoudar/neuron/nrnPara/missing --run makeinfo'
MAKE_RPMS_FALSE=''
MAKE_RPMS_TRUE='#'
MEMACSLIB=''
MEMACSLIBLA=''
METISINCLUDE=''
METISLIB=''
METISLIBADD=''
METISOBJADD=''
MINGW_CFLAG=''
MPICC='mpicc'
MPICXX=''
MPILIBS=''
NIDDK=''
NMODL_BUILD_FALSE='#'
NMODL_BUILD_TRUE=''
NMODL_ONLY_FALSE=''
NMODL_ONLY_TRUE='#'
NRNJAVA_DEP=''
NRNJAVA_LIBLA=''
NRNJAVA_LIBS=''
NRNMECH_DLL_STYLE_FALSE=''
NRNMECH_DLL_STYLE_TRUE=''
NRNNI_DEP=''
NRNNI_LIBLA=''
NRNNI_LIBS=''
NRNPURIFY_FALSE=''
NRNPURIFY_TRUE=''
NRNPYTHON_DEFINES=''
NRNPYTHON_DEP=''
NRNPYTHON_EXEC=''
NRNPYTHON_INCLUDES=''
NRNPYTHON_LIBLA=''
NRNPYTHON_LIBS=''
NRNPYTHON_PYLIBLINK=''
NRN_LIBDIR=''
NRN_READLINE_DEP=''
NRN_READLINE_LIBS=''
NRN_REALTIME_INCLUDE=''
NRN_SRCDIR='.'
OBJEXT='o'
PACKAGE='nrn'
PACKAGE_BUGREPORT=''
PACKAGE_NAME='nrn'
PACKAGE_STRING='nrn 7.1'
PACKAGE_TARNAME='nrn'
PACKAGE_VERSION='7.1'
PACKAGE_VERSION_MAJOR='7'
PACKAGE_VERSION_MINOR='1'
PATH_SEPARATOR=':'
PTHREAD_CC=''
PTHREAD_CFLAGS=''
PTHREAD_LIBS=''
PVM_INCLUDES=''
PVM_LIBS=''
PVM_XTRA_LIBS=''
RANLIB='ranlib'
READLINE_LIBS=''
RPM_ARGS=''
RPM_CONFIGURE_ARGS=''--prefix=/u/home/campus/vgoudar/neuron/nrnPara' '--without-iv' '--with-parnrn' '--with-mpi''
RPM_DIR=''
RPM_PROG=''
RPM_RELEASE='rel359'
RPM_TARBALL=''
RPM_TARGET=''
SED='/bin/sed'
SET_MAKE=''
SHELL='/bin/sh'
STRIP='strip'
TERMCAP_LIB=''
UniversalMacBinary_FALSE=''
UniversalMacBinary_TRUE='#'
VERSION='7.1'
X_CFLAGS=''
X_EXTRA_LIBS=''
X_LIBS=''
X_PRE_LIBS=''
YACC='bison -y'
_ACJNI_JAVAC=''
ac_ct_AR='ar'
ac_ct_CC='gcc'
ac_ct_CXX='g++'
ac_ct_F77='g77'
ac_ct_RANLIB='ranlib'
ac_ct_STRIP='strip'
acx_pthread_config=''
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-redhat-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='redhat'
datadir='${prefix}/share'
enable_carbon=''
exec_prefix='NONE'
host='x86_64-redhat-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='redhat'
includedir='${prefix}/include'
infodir='${prefix}/info'
install_sh='/u/home/campus/vgoudar/neuron/nrnPara/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
marshall_dir=''
mkdir_p='mkdir -p --'
nrndef_mac='//'
nrndef_mswin='//'
nrndef_unix='//'
oldincludedir='/usr/include'
prefix='/u/home/campus/vgoudar/neuron/nrnPara'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
setup_extra_link_args=''
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
uudecode=''

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

#define DISCRETE_EVENT_OBSERVER 1
#define HAVE_DLFCN_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRINGS_H 1
#define HAVE_STRING_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_UNISTD_H 1
#define IVOS_DECLARE_TRUE
#define PACKAGE "nrn"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_NAME "nrn"
#define PACKAGE_STRING "nrn 7.1"
#define PACKAGE_TARNAME "nrn"
#define PACKAGE_VERSION "7.1"
#define STDC_HEADERS 1
#define VERSION "7.1"
#define YYTEXT_POINTER 1
#endif
#ifdef __cplusplus
extern "C" void std::exit (int) throw (); using std::exit;

configure: exit 1
Im attempting to install neuron version 7.1. Is openmpi not supported? Is the cluster missing some libraries? Please advise.

hines
Site Admin
Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

Re: Installing neuron (nrn 7.1) with openmpi

Post by hines » Thu Feb 10, 2011 7:12 am

OpenMPI should work and I've used it myself.
By the way, to get all the parallel functionality, use --with-paranrn instead of --with-mpi .
From configure
checking for mpicc... mpicc
checking for MPI_Init... no
From config.log
configure:20694: checking for MPI_Init
configure:20751: mpicc -o conftest -g -O2 conftest.c -lm >&5
/u/local/mpi/openmpi/1.3.3_wofed1.4.1_intel11.1/lib/libmpi.a(btl_openib_endpoint.o): In function `mca_btl_openib_endpoint_destruct':
../../../../../ompi/mca/btl/openib/btl_openib_endpoint.c:(.text+0x807): undefined reference to `ibv_unreg_xrc_rcv_qp'
Perhaps openmpi is not installed properly.
Verify that you can run one of their test programs.
Also I would update to a more recent version of NEURON either from the
mercurial repository or from
http://www.neuron.yale.edu/ftp/neuron/versions/alpha/

vgoudar
Posts: 19
Joined: Fri Dec 03, 2010 3:41 am

Re: Installing neuron (nrn 7.1) with openmpi

Post by vgoudar » Tue Feb 15, 2011 10:15 pm

Hi Dr. Hines,

Thanks for the input. I did go back to the cluster admin and get their help installing it. Apparently, the modules werent loaded correctly. Im now running into a different problem while running on multiple processors with MPI on the cluster. Scripts run properly up until pc.runworker() and then freeze. This happened on nrn-7.1 and nrn-7.2 alpha. I tried running the scripts in src/parallel such as test1.hoc and test7.hoc. Since test0.hoc doesnt run in BBS mode, it runs to completion printing the ids of the different processors. But, the others seem to freeze. Could this be a problem with parallel context code? Can you please give me some clues on how this may be debugged?

Thanks.

hines
Site Admin
Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

Re: Installing neuron (nrn 7.1) with openmpi

Post by hines » Wed Feb 16, 2011 7:28 am

It is good that test0.hoc works.
Does test1.hoc work with one processor? ( mpiexec -n 1 nrniv -mpi test1.hoc )
or however you launch on your cluster.
If that works but not with -n 2 then diagnostic strategies are to see if it works with
mpich2, set the nrn/src/parallel/bbs.cpp:int BBSImpl::debug_ = 0;
rebuild and try to interpret what is printing, or add your own printf statements.
Is it possible for me to get a guest login on your cluster?

I will be out of town tomorrow til next wednesday so communication may be delayed.

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