esys-escript

I can not compile with openmpi

Asked by Kasemsak Saetang

My name is Kasemsak Saetang. I am a physics lecturer of Nakhon Si Thammarat Rajabhat University. I completely installed python-escript 4.0 without mpi on a high performance computer under Cent OS 7.0. Because my data took a lot of to run, I considered to use openmpi. I got a problem to set link against of mpi. I don't khow what a problem. My mpi version is openmpi-1.8.4.

My configuration is

# Flavour of MPI implementation
# Recognized values: 'none', 'MPT', 'MPICH', 'MPICH2', 'OPENMPI', 'INTELMPI'
# DEFAULT: 'none' (disable MPI)
mpi = 'OPENMPI'

# Prefix or paths to MPI headers and libraries. See note above about prefixes.
mpi_prefix = '/opt/openmpi-1.8.5/'

# MPI libraries to link against
#mpi_libs = ['mpi_cxx', 'mpi', 'open-rte', 'open-pal']

The error message is

Checking whether the C++ compiler works... (cached) yes
Checking for C++ function gethostname()... (cached) yes
Checking for C++ header file byteswap.h... (cached) yes
Checking for C++ function SCbswap32()... (cached) yes
Checking for C++ header file sys/endian.h... (cached) no
Checking for C++ header file libkern/OSByteOrder.h... (cached) no
Checking for C++ header file Python.h... (cached) yes
Checking for C++ function Py_Exit()... (cached) yes
Checking for C++ library boost_python-mt... (cached) yes
Checking for C++ header file numpy/ndarrayobject.h... (cached) yes
Checking for C++ library netcdf_c++... (cached) yes
Checking for C++ library siloh5... (cached) yes
Checking for C++ library mpi... no
RuntimeError: Unable to link against ['mpi'] (paths: /opt/openmpi-1.8.5/include, /opt/openmpi-1.8.5/lib):
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/SConstruct", line 518:
    env=checkOptionalLibraries(env)
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/dependencies.py", line 396:
    mpi_inc_path,mpi_lib_path=findLibWithHeader(env, env['mpi_libs'], 'mpi.h', env['mpi_prefix'], lang='c++')
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/site_init.py", line 75:
    raise RuntimeError('Unable to link against %s (paths: %s, %s)'%(libs,inc_path,lib_path))
[c10c0em@hydrogen python-escript_4.1~1]$

Please tell me how I can solve that ?

Sincerely,
Kasemsak Saetang

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Bob
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Revision history for this message
Joel Fenwick (j-fenwick1) said : 		#1

I haven't looked at this in great detail but you've said that your version is openmpi-1.8.4. But your config points to openmpi-1.8.5

Revision history for this message
Kasemsak Saetang (light2529) said : 		#2

I try to used many version but, it is the same problem. In our HPC, we can source mpich, mpich2, openmpi1.8.4, openmpi1.8.5 and mpich2 installed by Anaconda. I don't khow how to set mpi_libs = and which mpi version that I should use. I can run the code without mpi by set mpi = 'none'. It take a lot of time to run. I want to use mpi with run-escript -n 4 -p 16

Revision history for this message
Joel Fenwick (j-fenwick1) said : 		#3

Understood.

Revision history for this message
Manfred Hampl (m-hampl) said : 		#4

Do you have openmpi-devel installed?

Revision history for this message
Bob (caltinay) said : 		#5

I am quite confident that you need to link against mpi_cxx etc, so you may just have to uncomment the line that start with mpi_libs=...

But in order to help it might be useful to see the output in config.log

Revision history for this message
Kasemsak Saetang (light2529) said : 		#6

To Manfred Hamp
I am not a root user and don't have root passqord . I will ask a HPC staff.

To Cihan Altinay
I have used mpi_libs = ['mpi_cxx', 'mpi', 'open-rte', 'open-pal'] many time. I try to change mpi_libs = ['mpirun', 'mpif77', 'mpif90', 'mpifortl' It is not woking.

RuntimeError: Unable to link against ['mpi_cxx', 'mpi', 'open-rte', 'open-pal'] (paths: /opt/openmpi-1.8.5/include, /opt/openmpi-1.8.5/lib):
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/SConstruct", line 518:
    env=checkOptionalLibraries(env)
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/dependencies.py", line 396:
    mpi_inc_path,mpi_lib_path=findLibWithHeader(env, env['mpi_libs'], 'mpi.h', env['mpi_prefix'], lang='c++')
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/site_init.py", line 75:
    raise RuntimeError('Unable to link against %s (paths: %s, %s)'%(libs,inc_path,lib_path))

Revision history for this message
Bob (caltinay) said : 		#7

Ok, the command
mpicc -show
should show you the required libraries.
However, it would be best if you could copy/paste the relevant output from your config.log

Revision history for this message
Bob (caltinay) said : 		#8

Sorry, please use
mpicxx -show
instead.

Revision history for this message
Kasemsak Saetang (light2529) said : 		#9

[c10c0em@hydrogen python-escript_4.1~1]$ mpicxx -show
g++ -I/home/users/scratch/c10c0em/work/anaconda/installed/include -L/home/users/scratch/c10c0em/work/anaconda/installed/lib -lmpicxx -Wl,-rpath -Wl,/home/users/scratch/c10c0em/work/anaconda/installed/lib -Wl,--enable-new-dtags -lmpi

Revision history for this message
Kasemsak Saetang (light2529) said : 		#10

Now I reinstall openmpi.

 ./configure --prefix=/home/users/scratch/c10c0em/work/new_openmpi/openmpi-1.10.0/installed CXX=g++ FC=gfortran

[c10c0em@hydrogen installed]$ ls bin/
mpic++ mpifort-vt orte-ps otfmerge vtf90
mpicc mpirun orterun otfmerge-mpi vtfilter
mpiCC ompi-clean orte-server otfprint vtfiltergen
mpicc-vt ompi_info orte-submit otfprofile vtfiltergen-mpi
mpiCC-vt ompi-ps orte-top otfprofile-mpi vtfilter-mpi
mpic++-vt ompi-server oshcc otfshrink vtfort
mpicxx ompi-top oshfort shmemcc vtrun
mpicxx-vt opal_wrapper oshmem_info shmemfort vtsetup
mpiexec opari oshrun shmemrun vtsetup.jar
mpif77 ortecc otfaux vtc++ vtunify
mpif77-vt orte-clean otfcompress vtcc vtunify-mpi
mpif90 orted otfconfig vtCC vtwrapper
mpif90-vt orte-dvm otfdecompress vtcxx
mpifort orte-info otfinfo vtf77

After that

# Flavour of MPI implementation
# Recognized values: 'none', 'MPT', 'MPICH', 'MPICH2', 'OPENMPI', 'INTELMPI'
# DEFAULT: 'none' (disable MPI)
mpi = 'OPENMPI'

# Prefix or paths to MPI headers and libraries. See note above about prefixes.
mpi_prefix = '/home/users/scratch/c10c0em/work/new_openmpi/openmpi-1.10.0/installed'

# MPI libraries to link against
mpi_libs = ['mpi_cxx', 'mpi', 'open-rte', 'open-pal']

It is error again.

[c10c0em@hydrogen python-escript_4.1~1]$ scons -j1 options_file=scons/templates/centos7_0_options.py
scons: Reading SConscript files ...
Using options in scons/templates/centos7_0_options.py.
Checking whether the C++ compiler works... (cached) yes
Checking for C++ function gethostname()... (cached) yes
Checking for C++ header file byteswap.h... (cached) yes
Checking for C++ function SCbswap32()... (cached) yes
Checking for C++ header file sys/endian.h... (cached) no
Checking for C++ header file libkern/OSByteOrder.h... (cached) no
Checking for C++ header file Python.h... (cached) yes
Checking for C++ function Py_Exit()... (cached) yes
Checking for C++ library boost_python-mt... yes
Checking for C++ header file numpy/ndarrayobject.h... (cached) yes
Checking for C++ library netcdf_c++... yes
Checking for C++ library siloh5... yes
Checking for C++ library mpi_cxx... no
RuntimeError: Unable to link against ['mpi_cxx', 'mpi', 'open-rte', 'open-pal'] (paths: /home/users/scratch/c10c0em/work/new_openmpi/openmpi-1.10.0/installed/include, /home/users/scratch/c10c0em/work/new_openmpi/openmpi-1.10.0/installed/lib):
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/SConstruct", line 518:
    env=checkOptionalLibraries(env)
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/dependencies.py", line 396:
    mpi_inc_path,mpi_lib_path=findLibWithHeader(env, env['mpi_libs'], 'mpi.h', env['mpi_prefix'], lang='c++')
  File "/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/site_init.py", line 75:
    raise RuntimeError('Unable to link against %s (paths: %s, %s)'%(libs,inc_path,lib_path))

Revision history for this message
Kasemsak Saetang (light2529) said : 		#11

mpicxx -show
g++ -I/home/users/scratch/c10c0em/work/new_openmpi/openmpi-1.10.0/installed/include -pthread -Wl,-rpath -Wl,/home/users/scratch/c10c0em/work/new_openmpi/openmpi-1.10.0/installed/lib -Wl,--enable-new-dtags -L/home/users/scratch/c10c0em/work/new_openmpi/openmpi-1.10.0/installed/lib -lmpi_cxx -lmpi

Revision history for this message
Bob (caltinay) said : 		#12

At this stage we really need the compiler output from the config.log file. You can find this file in the escript source tree where you ran scons.

Revision history for this message
Kasemsak Saetang (light2529) said : 		#13

This is config.log

file /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/dependencies.py,line 35:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking whether the C++ compiler works...
scons: Configure: ".sconf_temp/conftest_0.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_0.cpp <-
  | |
  | |int main()
  | |{
  | | return 0;
  | |}
  | |
  |
g++ -o .sconf_temp/conftest_0.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -DSVN_VERSION=-2 -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_0.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function gethostname()...
scons: Configure: ".sconf_temp/conftest_1.cpp" is up to date.
scons: Configure: The original builder output was:
  |.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 -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -DSVN_VERSION=-2 -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_1.cpp
g++ -o .sconf_temp/conftest_1 -fopenmp .sconf_temp/conftest_1.o -L/home/users/scratch/c10c0em/work/anaconda/installed/lib
scons: Configure: yes

scons: Configure: Checking for C++ header file byteswap.h...
scons: Configure: ".sconf_temp/conftest_2.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_2.cpp <-
  | |
  | |#include "byteswap.h"
  | |
  | |
  |
g++ -o .sconf_temp/conftest_2.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_2.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function SCbswap32()...
scons: Configure: ".sconf_temp/conftest_3.cpp" is up to date.
scons: Configure: The original builder output was:
  |.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 -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_3.cpp
g++ -o .sconf_temp/conftest_3 -fopenmp .sconf_temp/conftest_3.o -L/home/users/scratch/c10c0em/work/anaconda/installed/lib
scons: Configure: yes

scons: Configure: Checking for C++ header file sys/endian.h...
scons: Configure: ".sconf_temp/conftest_4.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_4.cpp <-
  | |
  | |#include "sys/endian.h"
  | |
  | |
  |
g++ -o .sconf_temp/conftest_4.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_4.cpp
.sconf_temp/conftest_4.cpp:2:24: error: sys/endian.h: No such file or directory
scons: Configure: no

scons: Configure: Checking for C++ header file libkern/OSByteOrder.h...
scons: Configure: ".sconf_temp/conftest_5.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_5.cpp <-
  | |
  | |#include "libkern/OSByteOrder.h"
  | |
  | |
  |
g++ -o .sconf_temp/conftest_5.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_5.cpp
.sconf_temp/conftest_5.cpp:2:33: error: libkern/OSByteOrder.h: No such file or directory
scons: Configure: no

file /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/dependencies.py,line 139:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ header file Python.h...
scons: Configure: ".sconf_temp/conftest_6.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_6.cpp <-
  | |
  | |#include "Python.h"
  | |
  | |
  |
g++ -o .sconf_temp/conftest_6.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -isystem /home/users/scratch/c10c0em/work/anaconda/installed/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_6.cpp
scons: Configure: yes

scons: Configure: Checking for C++ function Py_Exit()...
scons: Configure: ".sconf_temp/conftest_7.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_7.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_7.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -isystem /home/users/scratch/c10c0em/work/anaconda/installed/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_7.cpp
g++ -o .sconf_temp/conftest_7 -fopenmp .sconf_temp/conftest_7.o -L/home/users/scratch/c10c0em/work/anaconda/installed/lib -lpython2.7
scons: Configure: yes

file /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/site_init.py,line 65:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library boost_python-mt...
scons: Configure: ".sconf_temp/conftest_8.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_8.cpp <-
  | |
  | |
  | |#include "boost/python.hpp"
  | |
  | |int
  | |main() {
  | |
  | |return 0;
  | |}
  | |
  |
g++ -o .sconf_temp/conftest_8.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -isystem /home/users/scratch/c10c0em/work/anaconda/installed/include/python2.7 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -I/home/users/scratch/c10c0em/work/anaconda/installed/include -Iboost_1_59_0 .sconf_temp/conftest_8.cpp
g++ -o .sconf_temp/conftest_8 -fopenmp .sconf_temp/conftest_8.o -L/home/users/scratch/c10c0em/work/anaconda/installed/lib -Lboost_1_59_0/stage/lib -lpython2.7 -lboost_python-mt -lboost_python-mt
scons: Configure: yes

file /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/dependencies.py,line 217:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ header file numpy/ndarrayobject.h...
scons: Configure: ".sconf_temp/conftest_9.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_9.cpp <-
  | |#include "Python.h"
  | |
  | |#include "numpy/ndarrayobject.h"
  | |
  | |
  |
g++ -o .sconf_temp/conftest_9.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -isystem /home/users/scratch/c10c0em/work/anaconda/installed/include/python2.7 -isystem /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/boost_1_59_0 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_9.cpp
scons: Configure: yes

file /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/site_init.py,line 65:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library netcdf_c++...
scons: Configure: ".sconf_temp/conftest_10.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_10.cpp <-
  | |
  | |
  | |#include "netcdf.h"
  | |
  | |int
  | |main() {
  | |
  | |return 0;
  | |}
  | |
  |
g++ -o .sconf_temp/conftest_10.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -isystem /home/users/scratch/c10c0em/work/anaconda/installed/include/python2.7 -isystem /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/boost_1_59_0 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DHAVE_NUMPY_H -I/home/users/scratch/c10c0em/work/anaconda/installed/include .sconf_temp/conftest_10.cpp
g++ -o .sconf_temp/conftest_10 -fopenmp .sconf_temp/conftest_10.o -L/home/users/scratch/c10c0em/work/anaconda/installed/lib -Lboost_1_59_0/stage/lib -L/usr/lib64 -lpython2.7 -lboost_python-mt -lnetcdf_c++ -lnetcdf -lnetcdf_c++
scons: Configure: yes

file /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/site_init.py,line 65:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library siloh5...
scons: Configure: ".sconf_temp/conftest_11.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_11.cpp <-
  | |
  | |
  | |#include "silo.h"
  | |
  | |int
  | |main() {
  | |
  | |return 0;
  | |}
  | |
  |
g++ -o .sconf_temp/conftest_11.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -isystem /home/users/scratch/c10c0em/work/anaconda/installed/include/python2.7 -isystem /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/boost_1_59_0 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DHAVE_NUMPY_H -DUSE_NETCDF -I/home/users/scratch/c10c0em/work/anaconda/installed/include -Isilo/silo-4.10.2/include .sconf_temp/conftest_11.cpp
g++ -o .sconf_temp/conftest_11 -fopenmp .sconf_temp/conftest_11.o -L/home/users/scratch/c10c0em/work/anaconda/installed/lib -Lboost_1_59_0/stage/lib -L/usr/lib64 -Lsilo/silo-4.10.2/lib -lpython2.7 -lboost_python-mt -lnetcdf_c++ -lnetcdf -lsiloh5 -lhdf5 -lsiloh5
scons: Configure: yes

file /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/site_scons/site_init.py,line 65:
 Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library mpi_cxx...
scons: Configure: ".sconf_temp/conftest_12.cpp" is up to date.
scons: Configure: The original builder output was:
  |.sconf_temp/conftest_12.cpp <-
  | |
  | |
  | |#include "mpi.h"
  | |
  | |int
  | |main() {
  | |
  | |return 0;
  | |}
  | |
  |
g++ -o .sconf_temp/conftest_12.o -c -Wextra -Wno-unused-parameter -fopenmp -g3 -fno-omit-frame-pointer -D_GLIBCXX_DEBUG -isystem /home/users/scratch/c10c0em/work/anaconda/installed/include/python2.7 -isystem /home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/boost_1_59_0 -DSVN_VERSION=-2 -DHAVE_GETHOSTNAME -DHAVE_BYTESWAP_H -DHAVE_NUMPY_H -DUSE_NETCDF -I/home/users/scratch/c10c0em/work/anaconda/installed/include -Isilo/silo-4.10.2/include -I/home/users/scratch/c10c0em/work/new_openmpi/openmpi-1.10.0/installed/include .sconf_temp/conftest_12.cpp
In file included from .sconf_temp/conftest_12.cpp:3:
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:18:19: error: metis.h: No such file or directory
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:33:4: error: #error "Incorrect user-supplied value fo IDXTYPEWIDTH"
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:42:4: error: #error "Incorrect user-supplied value fo REALTYPEWIDTH"
In file included from .sconf_temp/conftest_12.cpp:3:
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:66: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:66: error: 'vtxdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:66: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:66: error: 'xadj' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:66: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:66: error: 'adjncy' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:66: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:66: error: 'vwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'adjwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'wgtflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'ncon' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:67: error: 'nparts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'tpwgts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'ubvec' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'options' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'edgecut' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:68: error: 'part' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:69: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:69: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:69: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:72: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:72: error: 'vtxdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:72: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:72: error: 'xadj' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:72: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:72: error: 'adjncy' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:72: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:72: error: 'vwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'adjwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'wgtflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'ndims' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:73: error: 'xyz' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'ncon' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'nparts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'tpwgts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'ubvec' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:74: error: 'options' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:75: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:75: error: 'edgecut' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:75: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:75: error: 'part' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:75: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:75: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:75: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'vtxdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'ndims' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'xyz' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'part' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:78: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:81: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:81: error: 'vtxdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:81: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:81: error: 'xadj' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:81: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:81: error: 'adjncy' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:81: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:81: error: 'vwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'adjwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'wgtflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'ncon' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:82: error: 'nparts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:83: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:83: error: 'tpwgts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:83: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:83: error: 'ubvec' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:83: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:83: error: 'options' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:83: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:83: error: 'edgecut' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:84: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:84: error: 'part' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:84: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:84: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:84: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:87: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:87: error: 'vtxdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:87: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:87: error: 'xadj' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:87: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:87: error: 'adjncy' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:87: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:87: error: 'vwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'vsize' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'adjwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'wgtflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:88: error: 'ncon' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:89: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:89: error: 'nparts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:89: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:89: error: 'tpwgts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:89: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:89: error: 'ubvec' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:89: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:89: error: 'ipc2redist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: 'options' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: 'edgecut' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: 'part' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:90: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:93: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:93: error: 'elmdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:93: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:93: error: 'eptr' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:93: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:93: error: 'eind' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:93: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:93: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: 'ncommonnodes' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: 'xadj' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: 'adjncy' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:94: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:97: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:97: error: 'elmdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:97: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:97: error: 'eptr' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:97: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:97: error: 'eind' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:97: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:97: error: 'elmwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'wgtflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'ncon' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'ncommonnodes' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:98: error: 'nparts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'tpwgts' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'ubvec' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'options' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'edgecut' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:99: error: 'part' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:100: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:100: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:100: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:103: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:103: error: 'vtxdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:103: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:103: error: 'xadj' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:103: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:103: error: 'adjncy' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:103: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:103: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: 'options' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: 'order' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: 'sizes' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:104: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:107: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:107: error: 'vtxdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:107: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:107: error: 'xadj' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:107: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:107: error: 'adjncy' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:107: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:107: error: 'vwgt' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'mtype' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'rtype' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'p_nseps' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:108: error: 's_nseps' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:109: error: 'real_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:109: error: 'ubfrac' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:109: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:109: error: 'seed' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:109: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:109: error: 'dbglvl' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:109: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:109: error: 'order' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:110: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:110: error: 'sizes' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:110: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:110: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:110: error: initializer expression list treated as compound expression
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:113: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:113: error: 'vtxdist' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:113: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:113: error: 'xadj' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:113: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:113: error: 'adjncy' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:113: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:113: error: 'numflag' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: 'options' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: 'order' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: 'idx_t' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: 'sizes' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: expected primary-expression before '*' token
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: 'comm' was not declared in this scope
/home/users/scratch/c10c0em/work/anaconda/installed/include/parmetis.h:114: error: initializer expression list treated as compound expression
scons: Configure: no

Revision history for this message
Bob (caltinay) said : 		#14

There are two issues here:

Firstly, you need to remove the scons database when you change your options file or you will get bogus results.
To remove the scons database and intermediate files issue:
rm -r .sconsign.dblite .sconf_temp

Secondly, it appears the problem is actually a parmetis issue - you need to install metis *and* parmetis. It looks like metis is missing.

Cihan

Revision history for this message
Kasemsak Saetang (light2529) said : 		#15

Thanks Cihan Altinay, that solved my question.

Revision history for this message
Kasemsak Saetang (light2529) said : 		#16

It is running.
inv.GravityInversion: Setting cost function...
inv.GravityInversion: Setting cost function...
inv.GravityInversion: Setting cost function...
inv.GravityInversion: Setting cost function...
inv.GravityInversion: Setting cost function...
inv.GravityInversion: Starting solver...
inv.GravityInversion: Starting solver...
inv.GravityInversion: Starting solver...
inv.GravityInversion: Starting solver...
inv.GravityInversion: Starting solver...
 I am not not sure it ok or not. I can not compile with parmetis.
The installed results is
*** Config Summary (see config.log and <prefix>/lib/buildvars for details) ***
Escript/Finley revision -2
  Install prefix: /home/users/scratch/c10c0em/work/anaconda/installed
          Python: /home/users/scratch/c10c0em/work/anaconda/installed
           boost: ['/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/boost_1_59_0', '/home/users/scratch/c10c0em/escript_sang/python-escript_4.1~1/boost_1_59_0/stage/lib'] (Version 1.59.0)
           numpy: YES (with headers)
             MPI: YES (flavour: OPENMPI)
        ParMETIS: NO
          LAPACK: NO
            CUDA: NO
          openmp: YES
            gdal: YES
          netcdf: YES
          pyproj: YES
           scipy: YES
           sympy: YES
           debug: NO
       boomeramg: NO
         cppunit: NO
             mkl: NO
            papi: NO
            silo: NO
         umfpack: NO
           visit: NO
            gmsh: YES
            gzip: NO
  Treating warnings as errors

SUCCESS: build complete

Revision history for this message
Best Bob (caltinay) said : 		#17

Your installation is ok. Parmetis is not a requirement, it's only used to optimize domain decomposition for unstructured domains.
If you have any other questions please open a separate issue.

Revision history for this message
Kasemsak Saetang (light2529) said : 		#18

Thanks Cihan Altinay, that solved my question.