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#1 2020-06-25 12:43:52

corra
Member
Registered: 2008-06-03
Posts: 143

Med installation on CentOS failed

Dear all,

I am trying to compile Code Aster in CentOS (HPC). I cannot get past med installation:

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Code_Aster Setup version 14.4.0-1
Copyright (c) 2001-2019 EDF R&D - http://www.code-aster.org 
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Command line :
  /cineca/prod/opt/compilers/python/3.6.4/none/bin/python3.6 setup.py --nocache --prefix=/galileo/home/userexternal/cchisari/bin/aster install hdf5 med 
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--------------------------------------------------------------------------------
Reading config file '/galileo/home/userexternal/cchisari/bin/aster-full-src-14.4.0/setup.cfg'...
      ASTER_ROOT (from cfg) : '/opt/aster'
 PREFER_COMPILER (from cfg) : 'GNU'
        MAXDEPTH (from cfg) : 5
      USE_LOCATE (from cfg) : False
 PREFER_SHARED_LIBS (from cfg) : False

--------------------------------------------------------------------------------
      ASTER_ROOT (from arguments) : /galileo/home/userexternal/cchisari/bin/aster

--------------------------------------------------------------------------------
Installation on :

Kernel  on an 

Linux r033c01s03 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 
--------------------------------------------------------------------------------


--------------------------------------------------------------------------------
Checking for max command length...   32768.0
Checking for file... /usr/bin/file
Checking for ar... /usr/bin/ar
Checking for architecture... Linux / posix / x86_64
Checking for number of processors (core)... 36 (will use: make -j 8)
Checking for Code_Aster platform type... LINUX64
Checking for bash... /usr/bin/bash
Checking for Python version... 3.6.4
Checking for python3.6... no
Checking for libpython3.6.so... /galileo/prod/opt/compilers/python/3.6.4/none/lib/libpython3.6.so
Checking for Python.h... /usr/include/python2.7/Python.h
Checking for gcc... /usr/bin/gcc
Checking for /usr/bin/gcc configured installation directory... /usr/lib/gcc/x86_64-redhat-linux/4.8.5, /usr/bin
Checking for libpthread.so... /usr/lib/x86_64-redhat-linux6E/lib64/libpthread.so
Checking for libz.so... /usr/lib64/libz.so
Checking for libdl.so... /usr/lib/x86_64-redhat-linux6E/lib64/libdl.so
Checking for libutil.so... /usr/lib/x86_64-redhat-linux6E/lib64/libutil.so
Checking for libm.so... /usr/lib/x86_64-redhat-linux6E/lib64/libm.so

--------------------------------------------------------------------------------
Checking for default compiler (for all products)... 
Checking for GNU compilers... 
Checking for gcc... /usr/bin/gcc
Checking for compiler version... gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Checking for g++... /usr/bin/g++
Checking for compiler version... g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Checking for gfortran... /usr/bin/gfortran
Checking for compiler version... GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Checking for pthread... -L/usr/lib/x86_64-redhat-linux6E/lib64 -lpthread (already found)
Checking for z... -L/usr/lib64 -lz (already found)
Checking for liblapack.a... /galileo/prod/opt/libraries/lapack/3.6.1/gnu--6.1.0/lib/liblapack.a
Checking for libblas.a... /galileo/prod/opt/libraries/blas/3.6.0/gnu--6.1.0/lib/libblas.a
Checking for libstdc++.so... /usr/lib/gcc/x86_64-redhat-linux/4.8.2/libstdc++.so
<E>_ABNORMAL_ABORT error reading profile : /tmp/system.36354/temp.opt_env
Checking for CC (/usr/bin/gcc) supports '-fno-stack-protector' option... yes
Checking for fortran program if the gcc bug #51267 is fixed (using VOLATILE)... no
Checking for F90 (/usr/bin/gfortran) supports '-fno-tree-dse' option... yes
Checking for fortran program if the gcc bug #51267 is fixed with -fno-tree-dse option... no
---------- ERROR MESSAGE ---------- 
/usr/lib/gcc/x86_64-redhat-linux/4.8.2/libstdc++.so: undefined reference to `memcpy@GLIBC_2.14'
/usr/lib/gcc/x86_64-redhat-linux/4.8.2/libgfortran.so: undefined reference to `clock_gettime@GLIBC_2.17'
/usr/lib/gcc/x86_64-redhat-linux/4.8.2/libgfortran.so: undefined reference to `secure_getenv@GLIBC_2.17'
collect2: error: ld returned 1 exit status


-------------------------------------------------------------------------------
WARNING :
  The fortran test program checking the LOC function with a loop failed.

Reasons :
  - it is known to fail using GNU Fortran 4.6.1 (and may be other releases)
    but it should be fixed using '-fno-tree-dse option'.

Code_Aster will be compiled without error but will be unusable!
You must choose another compiler or change the optimization level.
You can cancel now or make the changes later in the config.txt file of
Code_Aster and rebuild it.
-------------------------------------------------------------------------------


Checking for C/fortran program using blas/lapack... no
---------- ERROR MESSAGE ---------- 
/usr/lib/gcc/x86_64-redhat-linux/4.8.2/libstdc++.so: undefined reference to `memcpy@GLIBC_2.14'
/usr/lib/gcc/x86_64-redhat-linux/4.8.2/libgfortran.so: undefined reference to `clock_gettime@GLIBC_2.17'
/usr/lib/gcc/x86_64-redhat-linux/4.8.2/libgfortran.so: undefined reference to `secure_getenv@GLIBC_2.17'
collect2: error: ld returned 1 exit status


-------------------------------------------------------------------------------
WARNING :
  The C/fortran test program calling blas and lapack subroutines failed.

Reasons :
  - unable to find suitable C/fortran compilers
  - blas/lapack libraries (or required by them) missing
  - incorrect compilation options

Nevertheless the compilation of Code_Aster may work !
If it failed, you must help the setup by setting CC, CFLAGS, MATHLIB...
-------------------------------------------------------------------------------


Checking for GNU compilers... yes
Checking for global values... 

Compiler variables (set as environment variables): 

export               CC='/usr/bin/gcc'
export           CFLAGS='-O2 -fno-stack-protector -fPIC'
export       CFLAGS_DBG='-g  -fno-stack-protector -fPIC'
export    CFLAGS_OPENMP='-fopenmp'
export              CXX='/usr/bin/g++'
export           CXXLIB='-L/usr/lib/gcc/x86_64-redhat-linux/4.8.2 -lstdc++'
export          DEFINED='LINUX64  _USE_OPENMP'
export              F90='/usr/bin/gfortran'
export         F90FLAGS='-O2 -fPIC -fno-tree-dse'
export     F90FLAGS_DBG='-g  -fPIC'
export      F90FLAGS_I8=' -fdefault-double-8 -fdefault-integer-8 -fdefault-real-8'
export  F90FLAGS_OPENMP=' -fopenmp'
export        FFLAGS_I8=' -fdefault-double-8 -fdefault-integer-8 -fdefault-real-8'
export               LD='/usr/bin/gfortran'
export   LDFLAGS_OPENMP=' -fopenmp'
export          MATHLIB='/galileo/prod/opt/libraries/lapack/3.6.1/gnu--6.1.0/lib/liblapack.a /galileo/prod/opt/libraries/blas/3.6.0/gnu--6.1.0/lib/libblas.a'
export         OTHERLIB='-L/usr/lib/x86_64-redhat-linux6E/lib64 -lpthread -L/usr/lib64 -lz'

# Environment settings :

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Checking for ps... /usr/bin/ps
Checking for xterm... /usr/bin/xterm
Checking for nedit... no
Checking for geany... no
Checking for gvim... no
Checking for gedit... /usr/bin/gedit
Checking for gdb... /usr/bin/gdb
Checking for ddd... no
Checking for flex... /usr/bin/flex
Checking for ranlib... /usr/bin/ranlib
Checking for bison... /usr/bin/bison
Checking for cmake... /galileo/prod/opt/tools/cmake/3.12.0/none/bin/cmake

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Checking for host name...   r033c01s03
Checking for network domain name...    galileo.cineca.it
Checking for full qualified network name...    r033c01s03.galileo.cineca.it

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Checking for dependencies and required variables for '__main__'...     [  OK  ]

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Checking for dependencies and required variables for '__cfg__'...      [  OK  ]
Filling cache...                                                       [  OK  ]

--------------------------------------------------------------------------------
Check if found values seem correct. If not you can change them using 'setup.cfg'.

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Compiler variables for hdf5 (set as environment variables):
export               CC='/usr/bin/gcc'
export           CFLAGS='-O2 -fno-stack-protector -fPIC'
export       CFLAGS_DBG='-g  -fno-stack-protector -fPIC'
export    CFLAGS_OPENMP='-fopenmp'
export              CXX='/usr/bin/g++'
export           CXXLIB='-L/usr/lib/gcc/x86_64-redhat-linux/4.8.2 -lstdc++'
export          DEFINED='LINUX64  _USE_OPENMP'
export              F90='/usr/bin/gfortran'
export         F90FLAGS='-O2 -fPIC -fno-tree-dse'
export     F90FLAGS_DBG='-g  -fPIC'
export      F90FLAGS_I8=' -fdefault-double-8 -fdefault-integer-8 -fdefault-real-8'
export  F90FLAGS_OPENMP=' -fopenmp'
export        FFLAGS_I8=' -fdefault-double-8 -fdefault-integer-8 -fdefault-real-8'
export               LD='/usr/bin/gfortran'
export   LDFLAGS_OPENMP=' -fopenmp'
export          MATHLIB='/galileo/prod/opt/libraries/lapack/3.6.1/gnu--6.1.0/lib/liblapack.a /galileo/prod/opt/libraries/blas/3.6.0/gnu--6.1.0/lib/libblas.a'
export         OTHERLIB='-L/usr/lib/x86_64-redhat-linux6E/lib64 -lpthread -L/usr/lib64 -lz'

# Environment settings :


--------------------------------------------------------------------------------
Checking for dependencies and required variables for 'hdf5'...         [  OK  ]

--------------------------------------------------------------------------------
Installation of   : hdf5 1.10.3
  HDF5 is a Hierarchical Data Format product consisting of a data format
  specification and a supporting library implementation. HDF5 is designed to
  address some of the limitations of the older HDF product and to address current
  and anticipated requirements of modern systems and applications.
Archive filename  : hdf5-1.10.3
Destination       : /galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3
Working directory : /tmp/install_hdf5.36354
--------------------------------------------------------------------------------

Filling cache...                                                       [  OK  ]
Checking permissions...                                                [  OK  ]

>>> Extraction <<<

entering directory '/tmp/install_hdf5.36354'
Extracting hdf5-1.10.3.tar.gz...                                       [  OK  ]
 --- 3206 files extracted
leaving directory '/tmp/install_hdf5.36354'

>>> Configuration <<<

entering directory '/tmp/install_hdf5.36354/hdf5-1.10.3'
Command line : unset LD ; CFLAGS=-std=gnu9x ./configure --prefix=/galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3
configure hdf5 installation...                                         
Command output :
configure hdf5 installation...                                         [  OK  ]
leaving directory '/tmp/install_hdf5.36354/hdf5-1.10.3'

>>> Building the product <<<

entering directory '/tmp/install_hdf5.36354/hdf5-1.10.3'
Command line : make -j 8
compiling hdf5...                                                      
Command output :
compiling hdf5...                                                      [  OK  ]
leaving directory '/tmp/install_hdf5.36354/hdf5-1.10.3'

>>> Installation <<<

entering directory '/tmp/install_hdf5.36354/hdf5-1.10.3'
Command line : make install
installing hdf5 to /galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3...
                                                                      
Command output :
installing hdf5 to /galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3...
                                                                      [  OK  ]
leaving directory '/tmp/install_hdf5.36354/hdf5-1.10.3'

>>> Installation <<<

entering directory '/galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3'
leaving directory '/galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3'

>>> Clean temporary objects <<<

entering directory '/tmp/install_hdf5.36354'
deleting /tmp/install_hdf5.36354/hdf5-1.10.3...                        [  OK  ]
deleting /tmp/install_hdf5.36354...
leaving directory '/tmp/install_hdf5.36354'
Filling cache...                                                       [  OK  ]

--------------------------------------------------------------------------------
Installation of hdf5 1.10.3 successfully completed
--------------------------------------------------------------------------------


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Compiler variables for med (set as environment variables):
export               CC='/usr/bin/gcc'
export           CFLAGS='-O2 -fno-stack-protector -fPIC'
export       CFLAGS_DBG='-g  -fno-stack-protector -fPIC'
export    CFLAGS_OPENMP='-fopenmp'
export              CXX='/usr/bin/g++'
export           CXXLIB='-L/usr/lib/gcc/x86_64-redhat-linux/4.8.2 -lstdc++'
export          DEFINED='LINUX64  _USE_OPENMP'
export              F90='/usr/bin/gfortran'
export         F90FLAGS='-O2 -fPIC -fno-tree-dse'
export     F90FLAGS_DBG='-g  -fPIC'
export      F90FLAGS_I8=' -fdefault-double-8 -fdefault-integer-8 -fdefault-real-8'
export  F90FLAGS_OPENMP=' -fopenmp'
export        FFLAGS_I8=' -fdefault-double-8 -fdefault-integer-8 -fdefault-real-8'
export               LD='/usr/bin/gfortran'
export   LDFLAGS_OPENMP=' -fopenmp'
export          MATHLIB='/galileo/prod/opt/libraries/lapack/3.6.1/gnu--6.1.0/lib/liblapack.a /galileo/prod/opt/libraries/blas/3.6.0/gnu--6.1.0/lib/libblas.a'
export         OTHERLIB='-L/usr/lib/x86_64-redhat-linux6E/lib64 -lpthread -L/usr/lib64 -lz'

# Environment settings :


--------------------------------------------------------------------------------
Checking for dependencies and required variables for 'med'...          [  OK  ]

--------------------------------------------------------------------------------
Installation of   : med 4.0.0
  MED-fichier (Modelisation et Echanges de Donnees, in English Modelisation
  and Data Exchange) is a library to store and exchange meshed data or computation results.
  It uses the HDF5 file format to store the data.
Archive filename  : med-4.0.0
Destination       : /galileo/home/userexternal/cchisari/bin/aster/public/med-4.0.0
Working directory : /tmp/install_med.36354
--------------------------------------------------------------------------------

Filling cache...                                                       [  OK  ]
Checking permissions...                                                [  OK  ]

>>> Extraction <<<

entering directory '/tmp/install_med.36354'
Extracting med-4.0.0.tar.gz...                                         [  OK  ]
 --- 6706 files extracted
leaving directory '/tmp/install_med.36354'

>>> Configuration <<<

entering directory '/tmp/install_med.36354/med-4.0.0'
Command line : unset LD ; export LDFLAGS='-Wl,--no-as-needed -L/usr/lib/x86_64-redhat-linux6E/lib64 -lpthread -L/usr/lib64 -lz -L/usr/lib/gcc/x86_64-redhat-linux/4.8.2 -lstdc++' ; export F77=$F90; export CXXFLAGS='-std=gnu++98'; export PATH=/tmp/tmpiida9huw:${PATH} ; ./configure  --disable-mesgerr --with-hdf5=/galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3 --prefix=/galileo/home/userexternal/cchisari/bin/aster/public/med-4.0.0
configure med installation...                                          
Command output :
configure med installation...                                          [FAILED]
Exit code : 77
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '32460' is supported by ustar format... yes
checking whether GID '25200' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
configure: Trying /galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3 home path for searching H5pubconf.h file.
checking for a sed that does not truncate output... /usr/bin/sed
checking whether to compile C using MPI... no
checking for style of include used by make... GNU
checking for gcc... /usr/bin/gcc
checking whether the C compiler works... no
configure: error: in `/tmp/install_med.36354/med-4.0.0':
configure: error: C compiler cannot create executables
See `config.log' for more details
EXIT_COMMAND_36354_00000074=77

 *** Exception raised : error during configure

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     SUMMARY OF INSTALLATION
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 Installation of   : hdf5 1.10.3
Destination       : /galileo/home/userexternal/cchisari/bin/aster/public/hdf5-1.10.3
Elapsed time      : 119.79 s
                                                                      [  OK  ]
 Installation of   : med 4.0.0
Destination       : /galileo/home/userexternal/cchisari/bin/aster/public/med-4.0.0
Elapsed time      : 3.68 s
                                                                      
*** Exception None raised : None
See detailed traceback in the logfile
                                                                       [FAILED]
Exit code : 4
 Installation of   : Code_Aster + 2 of its prerequisites 
Destination       : /galileo/home/userexternal/cchisari/bin/aster
Elapsed time      : 139.21 s
                                                                      [  OK  ]

I cannot understand what the error is about. Is anyone able to help please?
I also attach the setup.dbg file.

Thank you very much,

Corrado

Offline

#2 2020-06-25 20:12:30

AsterO'dactyle
Administrator
Registered: 2007-11-29
Posts: 334

Re: Med installation on CentOS failed

"The C/fortran test program calling blas and lapack subroutines failed."


Code_Asterの開発者

Offline

#3 2020-06-26 09:38:21

corra
Member
Registered: 2008-06-03
Posts: 143

Re: Med installation on CentOS failed

Thank you for your reply, but also:

Checking for liblapack.a... /galileo/prod/opt/libraries/lapack/3.6.1/gnu--6.1.0/lib/liblapack.a
Checking for libblas.a... /galileo/prod/opt/libraries/blas/3.6.0/gnu--6.1.0/lib/libblas.a

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