esys-escript

compile error with openmpi

Asked by hanzj

hello,all
I came across one problem when I tried to compile the python-escript5.1 on ubuntu 16.04. so i chose the xenial_options.py. I modified it as follows.
escript_opts_version = 203
openmp = True
boost_libs = ['boost_python-py27']
mpi = 'OPENMPI'
mpi_prefix = ['/usr/lib/openmpi','/usr/lib']
mpi_libs = ['mpi_cxx', 'mpi', 'open-rte', 'open-pal']
netcdf = True
umfpack = True
umfpack_prefix = ['/usr/include/suitesparse', '/usr/lib']
umfpack_libs = ['umfpack', 'blas', 'amd']
lapack_prefix = ['/usr/include/atlas', '/usr/lib/atlas-base']
dudley_assemble_flags = '-funroll-loops'
gmsh = True
gmsh_prefix = ['/home/han/gmsh/bin']

but when I use the command 'scons -j4 options_file=scons/templates/xenial_options.py', it paused at the stage, from the terminal, it reads as follows:
Linking build/posix/weipa/src/libescriptreader.so
Install file: "build/posix/weipa/src/libescriptreader.so" as "lib/libescriptreader.so"
/home/han/esys/bin/run-escript /home/han/esys/build/scripts/release_sanity.py
[Dura:15292] [[18645,0],0] tcp_peer_recv_connect_ack: received different version from [[18645,1],0]: 1.10.2 instead of 1.8.4

it stayed at the command line for a long time and can not continue.

anyone can figure out what the matter is ?
looking forwards to your reply

best regards

han zhijian

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Revision history for this message
hanzj (hanzj14) said : 		#1

the config.log shows as follows:
file /home/han/esys/site_scons/dependencies.py,line 48:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking whether the C++ compiler works...
.sconf_temp/conftest_0.cpp <-
  |
  |int main()
  |{
  | return 0;
  |}
  |
g++ -o .sconf_temp/conftest_0.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -Iinclude .sconf_temp/conftest_0.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function gethostname()...
.sconf_temp/conftest_1.cpp <-
  |
  |
  |#include <assert.h>
  |
  |#ifdef __cplusplus
  |extern "C"
  |#endif
  |char gethostname();
  |
  |int main() {
  |#if defined (__stub_gethostname) || defined (__stub___gethostname)
  | fail fail fail
  |#else
  | gethostname();
  |#endif
  |
  | return 0;
  |}
  |
g++ -o .sconf_temp/conftest_1.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -Iinclude .sconf_temp/conftest_1.cpp
g++ -o .sconf_temp/conftest_1 -fopenmp .sconf_temp/conftest_1.o -Llib
scons: Configure: yes

scons: Configure: Checking for C++ header file byteswap.h...
.sconf_temp/conftest_2.cpp <-
  |
  |#include "byteswap.h"
  |
  |
g++ -o .sconf_temp/conftest_2.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -Iinclude .sconf_temp/conftest_2.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function SCbswap32()...
.sconf_temp/conftest_3.cpp <-
  |
  |
  |#include <assert.h>
  |#include <byteswap.h>
  |#define SCbswap32() {int x=0;bswap_32(x);}
  |
  |int main() {
  |#if defined (__stub_SCbswap32) || defined (__stub___SCbswap32)
  | fail fail fail
  |#else
  | SCbswap32();
  |#endif
  |
  | return 0;
  |}
  |
g++ -o .sconf_temp/conftest_3.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -Iinclude .sconf_temp/conftest_3.cpp
g++ -o .sconf_temp/conftest_3 -fopenmp .sconf_temp/conftest_3.o -Llib
scons: Configure: yes

scons: Configure: Checking for C++ header file sys/endian.h...
.sconf_temp/conftest_4.cpp <-
  |
  |#include "sys/endian.h"
  |
  |
g++ -o .sconf_temp/conftest_4.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_4.cpp
.sconf_temp/conftest_4.cpp:2:24: fatal error: sys/endian.h: No such file or directory
compilation terminated.
scons: Configure: no

scons: Configure: Checking for C++ header file libkern/OSByteOrder.h...
.sconf_temp/conftest_5.cpp <-
  |
  |#include "libkern/OSByteOrder.h"
  |
  |
g++ -o .sconf_temp/conftest_5.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_5.cpp
.sconf_temp/conftest_5.cpp:2:33: fatal error: libkern/OSByteOrder.h: No such file or directory
compilation terminated.
scons: Configure: no

scons: Configure: Checking for working complex std::acos()...
.sconf_temp/conftest_6.cpp <-
  |
  |#include <complex>
  |int main() { std::complex<double> x(0,3.14159265359), y(1.5707963,-1.8622957);
  |return std::abs(std::acos(x)-y) < 1e-6 ? 0:-1;}
  |
g++ -o .sconf_temp/conftest_6.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_6.cpp
g++ -o .sconf_temp/conftest_6 -fopenmp .sconf_temp/conftest_6.o -Llib
.sconf_temp/conftest_6 > .sconf_temp/conftest_6.out
scons: Configure: yes

file /home/han/esys/site_scons/dependencies.py,line 167:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ header file Python.h...
.sconf_temp/conftest_7.cpp <-
  |
  |#include "Python.h"
  |
  |
g++ -o .sconf_temp/conftest_7.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_7.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function Py_Exit()...
.sconf_temp/conftest_8.cpp <-
  |
  |
  |#include <assert.h>
  |
  |#ifdef __cplusplus
  |extern "C"
  |#endif
  |char Py_Exit();
  |
  |int main() {
  |#if defined (__stub_Py_Exit) || defined (__stub___Py_Exit)
  | fail fail fail
  |#else
  | Py_Exit();
  |#endif
  |
  | return 0;
  |}
  |
g++ -o .sconf_temp/conftest_8.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_8.cpp
g++ -o .sconf_temp/conftest_8 -fopenmp .sconf_temp/conftest_8.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -lpython2.7
scons: Configure: yes

file /home/han/esys/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library boost_python-py27...
.sconf_temp/conftest_9.cpp <-
  |
  |
  |#include "boost/python.hpp"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_9.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude -I/usr/include .sconf_temp/conftest_9.cpp
g++ -o .sconf_temp/conftest_9 -fopenmp .sconf_temp/conftest_9.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lboost_python-py27 -lboost_python-py27
scons: Configure: yes

file /home/han/esys/site_scons/dependencies.py,line 244:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ header file numpy/ndarrayobject.h...
.sconf_temp/conftest_10.cpp <-
  |#include "Python.h"
  |
  |#include "numpy/ndarrayobject.h"
  |
  |
g++ -o .sconf_temp/conftest_10.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_10.cpp
In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1777:0,
                 from /usr/include/python2.7/numpy/ndarrayobject.h:18,
                 from .sconf_temp/conftest_10.cpp:3:
/usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
scons: Configure: yes

file /home/han/esys/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library netcdf_c++...
.sconf_temp/conftest_11.cpp <-
  |
  |
  |#include "netcdf.h"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_11.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DESYS_HAVE_NUMPY_H -Iinclude -I/usr/include .sconf_temp/conftest_11.cpp
g++ -o .sconf_temp/conftest_11 -fopenmp .sconf_temp/conftest_11.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lboost_python-py27 -lnetcdf_c++ -lnetcdf -lnetcdf_c++
scons: Configure: yes

file /home/han/esys/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library umfpack...
.sconf_temp/conftest_12.cpp <-
  |
  |
  |#include "umfpack.h"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_12.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DESYS_HAVE_NUMPY_H -DESYS_HAVE_NETCDF -Iinclude -I/usr/include -I/usr/include/suitesparse .sconf_temp/conftest_12.cpp
g++ -o .sconf_temp/conftest_12 -fopenmp .sconf_temp/conftest_12.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lboost_python-py27 -lumfpack -lblas -lamd -lumfpack
scons: Configure: yes

file /home/han/esys/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library mpi_cxx...
.sconf_temp/conftest_13.cpp <-
  |
  |
  |#include "mpi.h"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_13.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DESYS_HAVE_NUMPY_H -DESYS_HAVE_NETCDF -DESYS_HAVE_UMFPACK -Iinclude -I/usr/include -I/usr/include/suitesparse -I/usr/lib/openmpi .sconf_temp/conftest_13.cpp
g++ -o .sconf_temp/conftest_13 -fopenmp .sconf_temp/conftest_13.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lboost_python-py27 -lmpi_cxx -lmpi -lopen-rte -lopen-pal -lmpi_cxx
scons: Configure: yes

file /home/han/esys/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library boost_iostreams...
.sconf_temp/conftest_14.cpp <-
  |
  |
  |#include "boost/iostreams/filter/gzip.hpp"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_14.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DESYS_HAVE_NUMPY_H -DESYS_HAVE_NETCDF -DESYS_HAVE_UMFPACK -DESYS_MPI -DMPI_NO_CPPBIND -DMPICH_IGNORE_CXX_SEEK -DMPI_INCLUDED -DESYS_HAVE_GMSH -DESYS_GMSH_MPI -Iinclude -I/usr/include -I/usr/include/suitesparse -I/usr/lib/openmpi .sconf_temp/conftest_14.cpp
g++ -o .sconf_temp/conftest_14 -fopenmp .sconf_temp/conftest_14.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lboost_python-py27 -lmpi_cxx -lmpi -lopen-rte -lopen-pal -lboost_iostreams -lboost_iostreams
scons: Configure: yes

Revision history for this message
Lutz Gross (l-gross) said : 		#2

My first guess is that there is a problem with OpenMPI. Are you have to run other OpenMPI applications?

Revision history for this message
Bob (caltinay) said : 		#3

"1.10.2 instead of 1.8.4"

- looks like a version mismatch. What does the following output:

which mpirun
mpirun -V
dpkg -l | grep openmpi

Revision history for this message
liucheng83 (lcheng83) said : 		#4

Hi,
Sorry to add my similar problems as I compile my optional files with mpi = 'OPENMPI'
It comes out:
RuntimeError: Unable to link against ['mpi_cxx', 'mpi', 'open-rte', 'open-pal'] (paths: /usr/lib/openmpi/include, /usr/lib/openmpi/lib):
  File "/home/lc/win-share/vbshare/escript--FEM/src/SConstruct", line 495:
    env=checkOptionalLibraries(env)
  File "/home/lc/win-share/vbshare/escript--FEM/src/site_scons/dependencies.py", line 481:
    mpi_inc_path,mpi_lib_path=findLibWithHeader(env, env['mpi_libs'], 'mpi.h', env['mpi_prefix'], lang='c++')
  File "/home/lc/win-share/vbshare/escript--FEM/src/site_scons/site_init.py", line 77:
    raise RuntimeError('Unable to link against %s (paths: %s, %s)'%(libs,inc_path,lib_path))

And the config.log is:

file /home/lc/win-share/vbshare/escript--FEM/src/site_scons/dependencies.py,line 48:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking whether the C++ compiler works...
.sconf_temp/conftest_0.cpp <-
  |
  |int main()
  |{
  | return 0;
  |}
  |
g++ -o .sconf_temp/conftest_0.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -Iinclude .sconf_temp/conftest_0.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function gethostname()...
.sconf_temp/conftest_1.cpp <-
  |
  |
  |#include <assert.h>
  |
  |#ifdef __cplusplus
  |extern "C"
  |#endif
  |char gethostname();
  |
  |int main() {
  |#if defined (__stub_gethostname) || defined (__stub___gethostname)
  | fail fail fail
  |#else
  | gethostname();
  |#endif
  |
  | return 0;
  |}
  |
g++ -o .sconf_temp/conftest_1.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -Iinclude .sconf_temp/conftest_1.cpp
g++ -o .sconf_temp/conftest_1 -fopenmp .sconf_temp/conftest_1.o -Llib
scons: Configure: yes

scons: Configure: Checking for C++ header file byteswap.h...
.sconf_temp/conftest_2.cpp <-
  |
  |#include "byteswap.h"
  |
  |
g++ -o .sconf_temp/conftest_2.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -Iinclude .sconf_temp/conftest_2.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function SCbswap32()...
.sconf_temp/conftest_3.cpp <-
  |
  |
  |#include <assert.h>
  |#include <byteswap.h>
  |#define SCbswap32() {int x=0;bswap_32(x);}
  |
  |int main() {
  |#if defined (__stub_SCbswap32) || defined (__stub___SCbswap32)
  | fail fail fail
  |#else
  | SCbswap32();
  |#endif
  |
  | return 0;
  |}
  |
g++ -o .sconf_temp/conftest_3.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -Iinclude .sconf_temp/conftest_3.cpp
g++ -o .sconf_temp/conftest_3 -fopenmp .sconf_temp/conftest_3.o -Llib
scons: Configure: yes

scons: Configure: Checking for C++ header file sys/endian.h...
.sconf_temp/conftest_4.cpp <-
  |
  |#include "sys/endian.h"
  |
  |
g++ -o .sconf_temp/conftest_4.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_4.cpp
.sconf_temp/conftest_4.cpp:2:24: fatal error: sys/endian.h: No such file or directory
compilation terminated.
scons: Configure: no

scons: Configure: Checking for C++ header file libkern/OSByteOrder.h...
.sconf_temp/conftest_5.cpp <-
  |
  |#include "libkern/OSByteOrder.h"
  |
  |
g++ -o .sconf_temp/conftest_5.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_5.cpp
.sconf_temp/conftest_5.cpp:2:33: fatal error: libkern/OSByteOrder.h: No such file or directory
compilation terminated.
scons: Configure: no

scons: Configure: Checking for working complex std::acos()...
.sconf_temp/conftest_6.cpp <-
  |
  |#include <complex>
  |int main() { std::complex<double> x(0,3.14159265359), y(1.5707963,-1.8622957);
  |return std::abs(std::acos(x)-y) < 1e-6 ? 0:-1;}
  |
g++ -o .sconf_temp/conftest_6.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_6.cpp
g++ -o .sconf_temp/conftest_6 -fopenmp .sconf_temp/conftest_6.o -Llib
.sconf_temp/conftest_6 > .sconf_temp/conftest_6.out
scons: Configure: yes

file /home/lc/win-share/vbshare/escript--FEM/src/site_scons/dependencies.py,line 167:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ header file Python.h...
.sconf_temp/conftest_7.cpp <-
  |
  |#include "Python.h"
  |
  |
g++ -o .sconf_temp/conftest_7.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_7.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function Py_Exit()...
.sconf_temp/conftest_8.cpp <-
  |
  |
  |#include <assert.h>
  |
  |#ifdef __cplusplus
  |extern "C"
  |#endif
  |char Py_Exit();
  |
  |int main() {
  |#if defined (__stub_Py_Exit) || defined (__stub___Py_Exit)
  | fail fail fail
  |#else
  | Py_Exit();
  |#endif
  |
  | return 0;
  |}
  |
g++ -o .sconf_temp/conftest_8.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_8.cpp
g++ -o .sconf_temp/conftest_8 -fopenmp .sconf_temp/conftest_8.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -lpython2.7
scons: Configure: yes

file /home/lc/win-share/vbshare/escript--FEM/src/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library boost_python-py27...
.sconf_temp/conftest_9.cpp <-
  |
  |
  |#include "boost/python.hpp"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_9.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude -I/usr/include .sconf_temp/conftest_9.cpp
g++ -o .sconf_temp/conftest_9 -fopenmp .sconf_temp/conftest_9.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lboost_python-py27 -lboost_python-py27
scons: Configure: yes

file /home/lc/win-share/vbshare/escript--FEM/src/site_scons/dependencies.py,line 244:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ header file numpy/ndarrayobject.h...
.sconf_temp/conftest_10.cpp <-
  |#include "Python.h"
  |
  |#include "numpy/ndarrayobject.h"
  |
  |
g++ -o .sconf_temp/conftest_10.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -Iinclude .sconf_temp/conftest_10.cpp
In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1777:0,
                 from /usr/include/python2.7/numpy/ndarrayobject.h:18,
                 from .sconf_temp/conftest_10.cpp:3:
/usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
scons: Configure: yes

file /home/lc/win-share/vbshare/escript--FEM/src/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library netcdf_c++...
.sconf_temp/conftest_11.cpp <-
  |
  |
  |#include "netcdf.h"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_11.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DESYS_HAVE_NUMPY_H -Iinclude -I/usr/include .sconf_temp/conftest_11.cpp
g++ -o .sconf_temp/conftest_11 -fopenmp .sconf_temp/conftest_11.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lboost_python-py27 -lnetcdf_c++ -lnetcdf -lnetcdf_c++
scons: Configure: yes

file /home/lc/win-share/vbshare/escript--FEM/src/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library umfpack...
.sconf_temp/conftest_12.cpp <-
  |
  |
  |#include "umfpack.h"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_12.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DESYS_HAVE_NUMPY_H -DESYS_HAVE_NETCDF -Iinclude -I/usr/include -I/usr/include/suitesparse .sconf_temp/conftest_12.cpp
g++ -o .sconf_temp/conftest_12 -fopenmp .sconf_temp/conftest_12.o -Llib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lboost_python-py27 -lumfpack -lblas -lamd -lumfpack
scons: Configure: yes

file /home/lc/win-share/vbshare/escript--FEM/src/site_scons/site_init.py,line 66:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library mpi_cxx...
.sconf_temp/conftest_13.cpp <-
  |
  |
  |#include "mpi.h"
  |
  |int
  |main() {
  |
  |return 0;
  |}
  |
g++ -o .sconf_temp/conftest_13.o -c -fopenmp -O3 -std=c++11 -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions -isystem /usr/include/python2.7 -isystem /usr/include/boost -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DESYS_HAVE_NUMPY_H -DESYS_HAVE_NETCDF -DESYS_HAVE_UMFPACK -Iinclude -I/usr/include -I/usr/include/suitesparse -I/usr/lib/openmpi/include .sconf_temp/conftest_13.cpp
scons: Configure: Caught exception while building ".sconf_temp/conftest_13":

Traceback (most recent call last):
  File "/usr/lib/scons/SCons/Job.py", line 212, in start
    task.prepare()
  File "/usr/lib/scons/SCons/Taskmaster.py", line 197, in prepare
    t.prepare()
  File "/usr/lib/scons/SCons/Node/FS.py", line 3093, in prepare
    SCons.Node.Node.prepare(self)
  File "/usr/lib/scons/SCons/Node/__init__.py", line 723, in prepare
    raise SCons.Errors.StopError(msg % (i, self))
SCons.Errors.StopError: Implicit dependency `/usr/lib/libopen-rte.so' not found, needed by target `.sconf_temp/conftest_13'.
scons: Configure: no

Revision history for this message
liucheng83 (lcheng83) said : 		#5

$which mpirun
/usr/bin/mpirun
$ mpirun -V
mpirun (Open MPI) 1.10.2
$ dpkg -l | grep openmpi
ii libhdf5-openmpi-10:amd64 1.8.16+docs-4ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version
ii libopenmpi-dev 1.10.2-8ubuntu1 amd64 high performance message passing library -- header files
ii libopenmpi1.10 1.10.2-8ubuntu1 amd64 high performance message passing library -- shared library
ii openmpi-bin 1.10.2-8ubuntu1 amd64 high performance message passing library -- binaries
ii openmpi-common 1.10.2-8ubuntu1 all high performance message passing library -- common files

Revision history for this message
Bob (caltinay) said : 		#6

As in your other question #647829 I think your installation of OpenMPI is incomplete. Try reinstalling as suggested there.

Can you help with this problem?

Provide an answer of your own, or ask hanzj for more information if necessary.

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