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SU2: An Open-Source Suite for Multiphysics Simulation and Design
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Compilation issue with cgns #250

Closed AntoineD closed 8 years ago

AntoineD commented 8 years ago

Hello,

I the same issue with v4.1.0 as in #28, which has been closed but does not contain helpful information.

The cgns headers and libs (v3.2.1) are correctly detected by configure. Here is the output of make V=1:

Making all in externals
make[1]: Entering directory `/home/antodech/SU2-4.1.0/externals'
make[2]: Entering directory `/home/antodech/SU2-4.1.0/externals'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home/antodech/SU2-4.1.0/externals'
make[1]: Leaving directory `/home/antodech/SU2-4.1.0/externals'
Making all in Common/lib
make[1]: Entering directory `/home/antodech/SU2-4.1.0/Common/lib'
g++ -DPACKAGE_NAME=\"SU2\" -DPACKAGE_TARNAME=\"SU2\" -DPACKAGE_VERSION=\"4.1.0\" -DPACKAGE_STRING=\"SU2\ 4.1.0\" -DPACKAGE_BUGREPORT=\"su2code-dev@lists.stanford.edu\" -DPACKAGE_URL=\"https://github.com/su2code\" -DPACKAGE=\"SU2\" -DVERSION=\"4.1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_SHORT_INT=2 -DSIZEOF_INT=4 -DSIZEOF_UNSIGNED_INT=4 -DSIZEOF_LONG_INT=8 -DSIZEOF_FLOAT=4 -DSIZEOF_DOUBLE=8 -DSIZEOF_VOID_P=8 -I.    -DHAVE_CGNS -I/gshare/soft/code_saturne/4.0.0/prod/cgnslib_3.2.1/include  -g -O2 -MT libSU2_a-geometry_structure.o -MD -MP -MF .deps/libSU2_a-geometry_structure.Tpo -c -o libSU2_a-geometry_structure.o `test -f '../src/geometry_structure.cpp' || echo './'`../src/geometry_structure.cpp
../src/geometry_structure.cpp: In member function ‘void CPhysicalGeometry::Read_CGNS_Format_Parallel(CConfig*, std::string, short unsigned int, short unsigned int)’:
../src/geometry_structure.cpp:6727: error: ‘ZoneType_t’ was not declared in this scope
../src/geometry_structure.cpp:6727: error: expected ‘;’ before ‘zonetype’
../src/geometry_structure.cpp:6728: error: ‘DataType_t’ was not declared in this scope
../src/geometry_structure.cpp:6728: error: expected ‘;’ before ‘datatype’
../src/geometry_structure.cpp:6731: error: ‘ElementType_t’ was not declared in this scope
../src/geometry_structure.cpp:6731: error: expected ‘;’ before ‘elemType’
../src/geometry_structure.cpp:6938: error: ‘zonetype’ was not declared in this scope
../src/geometry_structure.cpp:7031: error: ‘datatype’ was not declared in this scope
../src/geometry_structure.cpp:7040: error: ‘datatype’ was not declared in this scope
../src/geometry_structure.cpp:7040: error: ‘RealDouble’ was not declared in this scope
../src/geometry_structure.cpp:7051: error: ‘datatype’ was not declared in this scope
../src/geometry_structure.cpp:7107: error: ‘elemType’ was not declared in this scope
../src/geometry_structure.cpp:7167: error: expected ‘;’ before ‘elmt_type’
../src/geometry_structure.cpp:7168: error: ‘elemType’ was not declared in this scope
../src/geometry_structure.cpp:7179: error: ‘elemType’ was not declared in this scope
../src/geometry_structure.cpp:7179: error: ‘MIXED’ was not declared in this scope
../src/geometry_structure.cpp:7180: error: ‘elmt_type’ was not declared in this scope
../src/geometry_structure.cpp:7185: error: ‘elmt_type’ was not declared in this scope
../src/geometry_structure.cpp:7204: error: ‘elmt_type’ was not declared in this scope
../src/geometry_structure.cpp:7205: error: ‘NODE’ was not declared in this scope
../src/geometry_structure.cpp:7209: error: ‘BAR_2’ was not declared in this scope
../src/geometry_structure.cpp:7213: error: ‘BAR_3’ was not declared in this scope
../src/geometry_structure.cpp:7217: error: ‘TRI_3’ was not declared in this scope
../src/geometry_structure.cpp:7221: error: ‘QUAD_4’ was not declared in this scope
../src/geometry_structure.cpp:7225: error: ‘TETRA_4’ was not declared in this scope
../src/geometry_structure.cpp:7229: error: ‘HEXA_8’ was not declared in this scope
../src/geometry_structure.cpp:7233: error: ‘PENTA_6’ was not declared in this scope
../src/geometry_structure.cpp:7237: error: ‘PYRA_5’ was not declared in this scope
../src/geometry_structure.cpp:7241: error: ‘HEXA_20’ was not declared in this scope
../src/geometry_structure.cpp:7259: error: ‘elemType’ was not declared in this scope
../src/geometry_structure.cpp:7350: error: ‘elemType’ was not declared in this scope
../src/geometry_structure.cpp:7367: error: ‘elemType’ was not declared in this scope
../src/geometry_structure.cpp:7374: error: ‘elemType’ was not declared in this scope
../src/geometry_structure.cpp:7375: error: ‘NODE’ was not declared in this scope
../src/geometry_structure.cpp:7378: error: ‘BAR_2’ was not declared in this scope
../src/geometry_structure.cpp:7381: error: ‘BAR_3’ was not declared in this scope
../src/geometry_structure.cpp:7384: error: ‘TRI_3’ was not declared in this scope
../src/geometry_structure.cpp:7387: error: ‘QUAD_4’ was not declared in this scope
../src/geometry_structure.cpp:7390: error: ‘TETRA_4’ was not declared in this scope
../src/geometry_structure.cpp:7393: error: ‘HEXA_8’ was not declared in this scope
../src/geometry_structure.cpp:7396: error: ‘PENTA_6’ was not declared in this scope
../src/geometry_structure.cpp:7399: error: ‘PYRA_5’ was not declared in this scope
../src/geometry_structure.cpp:7402: error: ‘HEXA_20’ was not declared in this scope
../src/geometry_structure.cpp:7415: error: ‘MIXED’ was not declared in this scope
../src/geometry_structure.cpp:7460: error: expected ‘;’ before ‘elmt_type’
../src/geometry_structure.cpp:7461: error: ‘elmt_type’ was not declared in this scope
../src/geometry_structure.cpp:8124: error: expected ‘;’ before ‘elmt_type’
../src/geometry_structure.cpp:8125: error: ‘elmt_type’ was not declared in this scope
../src/geometry_structure.cpp:8128: error: ‘NODE’ was not declared in this scope
../src/geometry_structure.cpp:8129: error: ‘BAR_2’ was not declared in this scope
../src/geometry_structure.cpp:8130: error: ‘BAR_3’ was not declared in this scope
../src/geometry_structure.cpp:8131: error: ‘TRI_3’ was not declared in this scope
../src/geometry_structure.cpp:8132: error: ‘QUAD_4’ was not declared in this scope
../src/geometry_structure.cpp:8133: error: ‘TETRA_4’ was not declared in this scope
../src/geometry_structure.cpp:8134: error: ‘HEXA_8’ was not declared in this scope
../src/geometry_structure.cpp:8135: error: ‘PENTA_6’ was not declared in this scope
../src/geometry_structure.cpp:8136: error: ‘PYRA_5’ was not declared in this scope
make[1]: *** [libSU2_a-geometry_structure.o] Error 1
make[1]: Leaving directory `/home/antodech/SU2-4.1.0/Common/lib'
make: *** [all-recursive] Error 1

Thx for your help.

economon commented 8 years ago

Hi,

Can you please share the console output during the configure step? I'd like to see more information about the compilation set up, including libraries and flags.

Tom

AntoineD commented 8 years ago

Hi,

here is the contents of config.log:

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

It was created by SU2 configure 4.1.0, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure --prefix=/gshare/work/hpascalj/CodeSU2-master --with-CGNS-lib=/gshare/soft/code_saturne/4.0.0/prod/cgnslib_3.2.1/lib --with-CGNS-include=/gshare/soft/code_saturne/4.0.0/prod/cgnslib_3.2.1/include

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

hostname = master
uname -m = x86_64
uname -r = 2.6.32-279.el6.x86_64
uname -s = Linux
uname -v = #1 SMP Wed Jun 13 18:24:36 EDT 2012

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

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

PATH: /opt/xcat/bin
PATH: /opt/xcat/sbin
PATH: /opt/pbs/default/bin
PATH: /opt/pbs/tools/bin
PATH: /usr/lpp/mmfs/bin/
PATH: /gshare/soft/star-ccm+/STAR-View+9.02.007
PATH: /gshare/soft/star-ccm+/STAR-CCM+9.02.007/star/bin
PATH: /opt/xcat/bin
PATH: /opt/xcat/sbin
PATH: /usr/lib64/qt-3.3/bin
PATH: /opt/pbs/default/bin
PATH: /opt/pbs/tools/bin
PATH: /usr/lpp/mmfs/bin/
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /sbin
PATH: /gshare/soft/init
PATH: /gshare/soft/scripts
PATH: .
PATH: /gshare/soft/init
PATH: /gshare/soft/scripts
PATH: .

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

configure:2465: checking build system type
configure:2479: result: x86_64-unknown-linux-gnu
configure:2499: checking host system type
configure:2512: result: x86_64-unknown-linux-gnu
configure:2532: checking target system type
configure:2545: result: x86_64-unknown-linux-gnu
configure:2587: checking for a BSD-compatible install
configure:2655: result: /usr/bin/install -c
configure:2666: checking whether build environment is sane
configure:2721: result: yes
configure:2872: checking for a thread-safe mkdir -p
configure:2911: result: /bin/mkdir -p
configure:2918: checking for gawk
configure:2934: found /bin/gawk
configure:2945: result: gawk
configure:2956: checking whether make sets $(MAKE)
configure:2978: result: yes
configure:3075: checking whether make supports nested variables
configure:3092: result: yes
configure:3117: checking for style of include used by make
configure:3145: result: GNU
configure:3196: result: >>> MPI support disabled by default <<<
configure:3269: checking for g++
configure:3285: found /usr/bin/g++
configure:3296: result: g++
configure:3323: checking for C++ compiler version
configure:3332: g++ --version >&5
g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
Copyright (C) 2010 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:3343: $? = 0
configure:3332: g++ -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) 
configure:3343: $? = 0
configure:3332: g++ -V >&5
g++: '-V' option must have argument
configure:3343: $? = 1
configure:3332: g++ -qversion >&5
g++: unrecognized option '-qversion'
g++: no input files
configure:3343: $? = 1
configure:3363: checking whether the C++ compiler works
configure:3385: g++    conftest.cpp  >&5
configure:3389: $? = 0
configure:3437: result: yes
configure:3440: checking for C++ compiler default output file name
configure:3442: result: a.out
configure:3448: checking for suffix of executables
configure:3455: g++ -o conftest    conftest.cpp  >&5
configure:3459: $? = 0
configure:3481: result: 
configure:3503: checking whether we are cross compiling
configure:3511: g++ -o conftest    conftest.cpp  >&5
configure:3515: $? = 0
configure:3522: ./conftest
configure:3526: $? = 0
configure:3541: result: no
configure:3546: checking for suffix of object files
configure:3568: g++ -c   conftest.cpp >&5
configure:3572: $? = 0
configure:3593: result: o
configure:3597: checking whether we are using the GNU C++ compiler
configure:3616: g++ -c   conftest.cpp >&5
configure:3616: $? = 0
configure:3625: result: yes
configure:3634: checking whether g++ accepts -g
configure:3654: g++ -c -g  conftest.cpp >&5
configure:3654: $? = 0
configure:3695: result: yes
configure:3720: checking dependency style of g++
configure:3831: result: gcc3
configure:3921: checking for gcc
configure:3937: found /usr/bin/gcc
configure:3948: result: gcc
configure:3979: checking for C compiler version
configure:3988: gcc --version >&5
gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
Copyright (C) 2010 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:3999: $? = 0
configure:3988: gcc -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) 
configure:3999: $? = 0
configure:3988: gcc -V >&5
gcc: '-V' option must have argument
configure:3999: $? = 1
configure:3988: gcc -qversion >&5
gcc: unrecognized option '-qversion'
gcc: no input files
configure:3999: $? = 1
configure:4003: checking whether we are using the GNU C compiler
configure:4022: gcc -c   conftest.c >&5
configure:4022: $? = 0
configure:4031: result: yes
configure:4040: checking whether gcc accepts -g
configure:4060: gcc -c -g  conftest.c >&5
configure:4060: $? = 0
configure:4101: result: yes
configure:4118: checking for gcc option to accept ISO C89
configure:4181: gcc  -c -g -O2  conftest.c >&5
configure:4181: $? = 0
configure:4194: result: none needed
configure:4216: checking dependency style of gcc
configure:4327: result: gcc3
configure:4345: checking whether gcc and cc understand -c and -o together
configure:4376: gcc -c conftest.c -o conftest2.o >&5
configure:4380: $? = 0
configure:4386: gcc -c conftest.c -o conftest2.o >&5
configure:4390: $? = 0
configure:4401: cc -c conftest.c >&5
configure:4405: $? = 0
configure:4413: cc -c conftest.c -o conftest2.o >&5
configure:4417: $? = 0
configure:4423: cc -c conftest.c -o conftest2.o >&5
configure:4427: $? = 0
configure:4445: result: yes
configure:4513: checking for ranlib
configure:4529: found /usr/bin/ranlib
configure:4540: result: ranlib
configure:4574: checking how to run the C preprocessor
configure:4605: gcc -E  conftest.c
configure:4605: $? = 0
configure:4619: gcc -E  conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:4619: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "SU2"
| #define PACKAGE_TARNAME "SU2"
| #define PACKAGE_VERSION "4.1.0"
| #define PACKAGE_STRING "SU2 4.1.0"
| #define PACKAGE_BUGREPORT "su2code-dev@lists.stanford.edu"
| #define PACKAGE_URL "https://github.com/su2code"
| #define PACKAGE "SU2"
| #define VERSION "4.1.0"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:4644: result: gcc -E
configure:4664: gcc -E  conftest.c
configure:4664: $? = 0
configure:4678: gcc -E  conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:4678: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "SU2"
| #define PACKAGE_TARNAME "SU2"
| #define PACKAGE_VERSION "4.1.0"
| #define PACKAGE_STRING "SU2 4.1.0"
| #define PACKAGE_BUGREPORT "su2code-dev@lists.stanford.edu"
| #define PACKAGE_URL "https://github.com/su2code"
| #define PACKAGE "SU2"
| #define VERSION "4.1.0"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:4707: checking for grep that handles long lines and -e
configure:4765: result: /bin/grep
configure:4770: checking for egrep
configure:4832: result: /bin/grep -E
configure:4837: checking for ANSI C header files
configure:4857: gcc -c -g -O2  conftest.c >&5
configure:4857: $? = 0
configure:4930: gcc -o conftest -g -O2   conftest.c  >&5
configure:4930: $? = 0
configure:4930: ./conftest
configure:4930: $? = 0
configure:4941: result: yes
configure:4954: checking for sys/types.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4954: checking for sys/stat.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4954: checking for stdlib.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4954: checking for string.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4954: checking for memory.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4954: checking for strings.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4954: checking for inttypes.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4954: checking for stdint.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4954: checking for unistd.h
configure:4954: gcc -c -g -O2  conftest.c >&5
configure:4954: $? = 0
configure:4954: result: yes
configure:4970: checking size of short int
configure:4975: gcc -o conftest -g -O2   conftest.c  >&5
configure:4975: $? = 0
configure:4975: ./conftest
configure:4975: $? = 0
configure:4989: result: 2
configure:5003: checking size of int
configure:5008: gcc -o conftest -g -O2   conftest.c  >&5
configure:5008: $? = 0
configure:5008: ./conftest
configure:5008: $? = 0
configure:5022: result: 4
configure:5036: checking size of unsigned int
configure:5041: gcc -o conftest -g -O2   conftest.c  >&5
configure:5041: $? = 0
configure:5041: ./conftest
configure:5041: $? = 0
configure:5055: result: 4
configure:5069: checking size of long int
configure:5074: gcc -o conftest -g -O2   conftest.c  >&5
configure:5074: $? = 0
configure:5074: ./conftest
configure:5074: $? = 0
configure:5088: result: 8
configure:5102: checking size of float
configure:5107: gcc -o conftest -g -O2   conftest.c  >&5
configure:5107: $? = 0
configure:5107: ./conftest
configure:5107: $? = 0
configure:5121: result: 4
configure:5135: checking size of double
configure:5140: gcc -o conftest -g -O2   conftest.c  >&5
configure:5140: $? = 0
configure:5140: ./conftest
configure:5140: $? = 0
configure:5154: result: 8
configure:5168: checking size of void *
configure:5173: gcc -o conftest -g -O2   conftest.c  >&5
configure:5173: $? = 0
configure:5173: ./conftest
configure:5173: $? = 0
configure:5187: result: 8
configure:5409: checking X11/Intrinsic.h usability
configure:5409: gcc -c -g -O2  conftest.c >&5
conftest.c:61:27: error: X11/Intrinsic.h: No such file or directory
configure:5409: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "SU2"
| #define PACKAGE_TARNAME "SU2"
| #define PACKAGE_VERSION "4.1.0"
| #define PACKAGE_STRING "SU2 4.1.0"
| #define PACKAGE_BUGREPORT "su2code-dev@lists.stanford.edu"
| #define PACKAGE_URL "https://github.com/su2code"
| #define PACKAGE "SU2"
| #define VERSION "4.1.0"
| #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 SIZEOF_SHORT_INT 2
| #define SIZEOF_INT 4
| #define SIZEOF_UNSIGNED_INT 4
| #define SIZEOF_LONG_INT 8
| #define SIZEOF_FLOAT 4
| #define SIZEOF_DOUBLE 8
| #define SIZEOF_VOID_P 8
| /* end confdefs.h.  */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| #  include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| #  include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| #include <X11/Intrinsic.h>
configure:5409: result: no
configure:5409: checking X11/Intrinsic.h presence
configure:5409: gcc -E  conftest.c
conftest.c:28:27: error: X11/Intrinsic.h: No such file or directory
configure:5409: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "SU2"
| #define PACKAGE_TARNAME "SU2"
| #define PACKAGE_VERSION "4.1.0"
| #define PACKAGE_STRING "SU2 4.1.0"
| #define PACKAGE_BUGREPORT "su2code-dev@lists.stanford.edu"
| #define PACKAGE_URL "https://github.com/su2code"
| #define PACKAGE "SU2"
| #define VERSION "4.1.0"
| #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 SIZEOF_SHORT_INT 2
| #define SIZEOF_INT 4
| #define SIZEOF_UNSIGNED_INT 4
| #define SIZEOF_LONG_INT 8
| #define SIZEOF_FLOAT 4
| #define SIZEOF_DOUBLE 8
| #define SIZEOF_VOID_P 8
| /* end confdefs.h.  */
| #include <X11/Intrinsic.h>
configure:5409: result: no
configure:5409: checking for X11/Intrinsic.h
configure:5409: result: no
configure:5721: checking for /gshare/soft/code_saturne/4.0.0/prod/cgnslib_3.2.1/lib/libcgns.a
configure:5735: result: yes
configure:5755: checking for /gshare/soft/code_saturne/4.0.0/prod/cgnslib_3.2.1/include/cgnslib.h
configure:5769: result: yes
configure:6815: checking that generated files are newer than configure
configure:6821: result: done
configure:6952: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by SU2 config.status 4.1.0, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  CONFIG_FILES    = 
  CONFIG_HEADERS  = 
  CONFIG_LINKS    = 
  CONFIG_COMMANDS = 
  $ ./config.status 

on master

config.status:875: creating externals/tecio/Makefile
config.status:875: creating externals/metis/Makefile
config.status:875: creating externals/parmetis/Makefile
config.status:875: creating Makefile
config.status:875: creating externals/Makefile
config.status:875: creating Common/lib/Makefile
config.status:875: creating SU2_CFD/obj/Makefile
config.status:875: creating SU2_DOT/obj/Makefile
config.status:875: creating SU2_MSH/obj/Makefile
config.status:875: creating SU2_DEF/obj/Makefile
config.status:875: creating SU2_SOL/obj/Makefile
config.status:875: creating SU2_GEO/obj/Makefile
config.status:875: creating SU2_PY/Makefile
config.status:1047: executing depfiles commands
configure:8181: result:

-------------------------------------------------------------------------
|    ___ _   _ ___                                                      |
|   / __| | | |_  )   Release 4.1.0 'Cardinal'                          |
|   \__ \ |_| |/ /                                                      |
|   |___/\___//___|   Suite                                             |
|                                                                       |
-------------------------------------------------------------------------
| SU2 Lead Dev.: Dr. Francisco Palacios, Francisco.D.Palacios@boeing.com|
|                Dr. Thomas D. Economon, economon@stanford.edu          |
-------------------------------------------------------------------------
| SU2 Developers:                                                       |
| - Prof. Juan J. Alonso's group at Stanford University.                |
| - Prof. Piero Colonna's group at Delft University of Technology.      |
| - Prof. Nicolas R. Gauger's group at Kaiserslautern U. of Technology. |
| - Prof. Alberto Guardone's group at Polytechnic University of Milan.  |
| - Prof. Rafael Palacios' group at Imperial College London.            |
-------------------------------------------------------------------------
| Copyright (C) 2012-2015 SU2, the open-source CFD code.                |
|                                                                       |
| SU2 is free software; you can redistribute it and/or                  |
| modify it under the terms of the GNU Lesser General Public            |
| License as published by the Free Software Foundation; either          |
| version 2.1 of the License, or (at your option) any later version.    |
|                                                                       |
| SU2 is distributed in the hope that it will be useful,                |
| but WITHOUT ANY WARRANTY; without even the implied warranty of        |
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU      |
| Lesser General Public License for more details.                       |
|                                                                       |
| You should have received a copy of the GNU Lesser General Public      |
| License along with SU2. If not, see <http://www.gnu.org/licenses/>.   |
-------------------------------------------------------------------------

Build Configuration Summary:

    Source code location: /home/antodech/SU2-4.1.0
    Install location:     /gshare/work/hpascalj/CodeSU2-master
    Version:              4.1.0
    C++ Compiler:         g++
    C Compiler:           gcc
    Preprocessor flags:   
    Compiler flags:       -g -O2
    Linker flags:         
    MPI support:          no
    Metis support:        no
    Parmetis support:     no
    TecIO support:        no
    CGNS support:         yes
    HDF5 support:         no
    SZIP support:         no
    ZLIB support:         no
    Mutation++ support:   no
    Jsoncpp support:      no
    LAPACK support:       no
    Datatype support:
        double              yes
        complex             no
        codi_reverse        no
        codi_forward        no

    External includes:    
    External libs:        

    Build SU2_CFD:        yes
    Build SU2_DOT:        yes
    Build SU2_MSH:        yes
    Build SU2_DEF:        yes
    Build SU2_SOL:        yes
    Build SU2_GEO:        yes

Please be sure to add the $SU2_HOME and $SU2_RUN environment variables,
and update your $PATH (and $PYTHONPATH if applicable) with $SU2_RUN.

Based on the input to this configuration, add these lines to your .bashrc file:

export SU2_RUN="/gshare/work/hpascalj/CodeSU2-master/bin"
export SU2_HOME="/home/antodech/SU2-4.1.0"
export PATH=$PATH:$SU2_RUN
export PYTHONPATH=$PYTHONPATH:$SU2_RUN

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

ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
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_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_file__gshare_soft_code_saturne_4_0_0_prod_cgnslib_3_2_1_include_cgnslib_h=yes
ac_cv_file__gshare_soft_code_saturne_4_0_0_prod_cgnslib_3_2_1_lib_libcgns_a=yes
ac_cv_header_X11_Intrinsic_h=no
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_objext=o
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_gcc_c_o=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_sizeof_double=8
ac_cv_sizeof_float=4
ac_cv_sizeof_int=4
ac_cv_sizeof_long_int=8
ac_cv_sizeof_short_int=2
ac_cv_sizeof_unsigned_int=4
ac_cv_sizeof_void_p=8
ac_cv_target=x86_64-unknown-linux-gnu
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_make_support_nested_variables=yes

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

ACLOCAL='${SHELL} /home/antodech/SU2-4.1.0/missing --run aclocal-1.12'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='0'
AM_V='$(V)'
AUTOCONF='${SHELL} /home/antodech/SU2-4.1.0/missing --run autoconf'
AUTOHEADER='${SHELL} /home/antodech/SU2-4.1.0/missing --run autoheader'
AUTOMAKE='${SHELL} /home/antodech/SU2-4.1.0/missing --run automake-1.12'
AWK='gawk'
BUILD_CFD_FALSE='#'
BUILD_CFD_TRUE=''
BUILD_CGNS_FALSE='#'
BUILD_CGNS_TRUE=''
BUILD_DEF_FALSE='#'
BUILD_DEF_TRUE=''
BUILD_DIRECTDIFF_FALSE=''
BUILD_DIRECTDIFF_TRUE='#'
BUILD_DOT_FALSE='#'
BUILD_DOT_TRUE=''
BUILD_GEO_FALSE='#'
BUILD_GEO_TRUE=''
BUILD_HDF5_FALSE=''
BUILD_HDF5_TRUE='#'
BUILD_JSONCPP_FALSE=''
BUILD_JSONCPP_TRUE='#'
BUILD_LAPACK_FALSE=''
BUILD_LAPACK_TRUE='#'
BUILD_METIS_FALSE=''
BUILD_METIS_TRUE='#'
BUILD_MSH_FALSE='#'
BUILD_MSH_TRUE=''
BUILD_MUTATIONPP_FALSE=''
BUILD_MUTATIONPP_TRUE='#'
BUILD_NORMAL_FALSE='#'
BUILD_NORMAL_TRUE=''
BUILD_PARMETIS_FALSE=''
BUILD_PARMETIS_TRUE='#'
BUILD_REVERSE_FALSE=''
BUILD_REVERSE_TRUE='#'
BUILD_SOL_FALSE='#'
BUILD_SOL_TRUE=''
BUILD_SZIP_FALSE=''
BUILD_SZIP_TRUE='#'
BUILD_TECIO_FALSE=''
BUILD_TECIO_TRUE='#'
BUILD_ZLIB_FALSE=''
BUILD_ZLIB_TRUE='#'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CGNS_CXX='-DHAVE_CGNS -I/gshare/soft/code_saturne/4.0.0/prod/cgnslib_3.2.1/include'
CGNS_LD='/gshare/soft/code_saturne/4.0.0/prod/cgnslib_3.2.1/lib/libcgns.a'
CPP='gcc -E'
CPPFLAGS=''
CXX='g++'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DEFS='-DPACKAGE_NAME=\"SU2\" -DPACKAGE_TARNAME=\"SU2\" -DPACKAGE_VERSION=\"4.1.0\" -DPACKAGE_STRING=\"SU2\ 4.1.0\" -DPACKAGE_BUGREPORT=\"su2code-dev@lists.stanford.edu\" -DPACKAGE_URL=\"https://github.com/su2code\" -DPACKAGE=\"SU2\" -DVERSION=\"4.1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_SHORT_INT=2 -DSIZEOF_INT=4 -DSIZEOF_UNSIGNED_INT=4 -DSIZEOF_LONG_INT=8 -DSIZEOF_FLOAT=4 -DSIZEOF_DOUBLE=8 -DSIZEOF_VOID_P=8'
DEPDIR='.deps'
DIRECTDIFF_CXX=''
DIRECTDIFF_LIBS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
GREP='/bin/grep'
HDF5_CXX=''
HDF5_LD=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
JSONCPP_CXX=''
JSONCPP_LD=''
LAPACK_CXX=''
LAPACK_LD=''
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/antodech/SU2-4.1.0/missing --run makeinfo'
METIS_INCLUDE=''
METIS_LIB=''
MKDIR_P='/bin/mkdir -p'
MUTATIONPP_CXX=''
MUTATIONPP_LD=''
OBJEXT='o'
PACKAGE='SU2'
PACKAGE_BUGREPORT='su2code-dev@lists.stanford.edu'
PACKAGE_NAME='SU2'
PACKAGE_STRING='SU2 4.1.0'
PACKAGE_TARNAME='SU2'
PACKAGE_URL='https://github.com/su2code'
PACKAGE_VERSION='4.1.0'
PARMETIS_INCLUDE=''
PARMETIS_LIB=''
PATH_SEPARATOR=':'
RANLIB='ranlib'
REVERSE_CXX=''
REVERSE_LIBS=''
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
SU2_METIS_CPPFLAGS=''
SU2_PARMETIS_CPPFLAGS=''
SZIP_CXX=''
SZIP_LD=''
TECIO_CPPFLAGS=''
TECIO_INCLUDE=''
VERSION='4.1.0'
ZLIB_CXX=''
ZLIB_LD=''
ac_ct_CC='gcc'
ac_ct_CXX='g++'
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep='_no'
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /home/antodech/SU2-4.1.0/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/gshare/work/hpascalj/CodeSU2-master'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
su2_externals_INCLUDES=''
su2_externals_LIBS=''
sysconfdir='${prefix}/etc'
target='x86_64-unknown-linux-gnu'
target_alias=''
target_cpu='x86_64'
target_os='linux-gnu'
target_vendor='unknown'

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

/* confdefs.h */
#define PACKAGE_NAME "SU2"
#define PACKAGE_TARNAME "SU2"
#define PACKAGE_VERSION "4.1.0"
#define PACKAGE_STRING "SU2 4.1.0"
#define PACKAGE_BUGREPORT "su2code-dev@lists.stanford.edu"
#define PACKAGE_URL "https://github.com/su2code"
#define PACKAGE "SU2"
#define VERSION "4.1.0"
#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 SIZEOF_SHORT_INT 2
#define SIZEOF_INT 4
#define SIZEOF_UNSIGNED_INT 4
#define SIZEOF_LONG_INT 8
#define SIZEOF_FLOAT 4
#define SIZEOF_DOUBLE 8
#define SIZEOF_VOID_P 8

configure: exit 0
economon commented 8 years ago

It looks like you're using a version of the CGNS lib that was provided by a different solver. Did you compile/install the CGNS portion yourself? I am wondering if this is a custom or modified version that isn't compatible. If you download and install a stand alone copy of CGNS (http://cgns.github.io/download.html) does it work?

AntoineD commented 8 years ago

We finally got it compiled, I'm closing this issue.