Hi,
I'm currently trying to compile Relion 1.2 on an LSF cluster based on
the Platform MPI (PMPI) implementation. $PATH, $LD_LIBRARY_PATH and
$MPICXX are set according to our local installation of PMPI. When
running INSTALL.sh -j 4 I get the following output:
----------------
# ./INSTALL.sh -j 4
Compiling fftw-3.2.2 ...
See
/g/software/linux/pack/relion-1.2/SRC/relion-1.2/external/fftw_build.log
for details
Compiling fltk-1.3.0 ...
See
/g/software/linux/pack/relion-1.2/SRC/relion-1.2/external/fltk_build.log
for details
configure: WARNING: Ignoring libraries " -lSM -lICE" requested by configure.
Compiling relion ...
See /g/software/linux/pack/relion-1.2/SRC/relion-1.2/relion_build.log
for details
src/metadata_container.cpp: In member function 'void
MetaDataContainer::insertVoidPtr(EMDLabel, void*)':
src/metadata_container.cpp:155: warning: deleting 'void*' is undefined
In file included from /opt/platform_mpi/include/mpi.h:1633,
from ./src/mpi.h:47,
from src/mpi.cpp:46:
/opt/platform_mpi/include/mpiCC.h:32:2: warning: #warning The entire set
of C++ language bindings have been deprecated in mpi 2.2 To disable this
warning use -Wno-deprecated.
src/mpi.cpp: In member function 'void MpiNode::report_MPI_ERROR(int)':
src/mpi.cpp:195: error: 'stderr' was not declared in this scope
src/mpi.cpp:195: error: 'fprintf' was not declared in this scope
make[1]: *** [src/mpi.lo] Error 1
make[1]: *** Waiting for unfinished jobs....
make: *** [all] Error 2
In file included from /opt/platform_mpi/include/mpi.h:1633,
from ./src/mpi.h:47,
from src/mpi.cpp:46:
/opt/platform_mpi/include/mpiCC.h:32:2: warning: #warning The entire set
of C++ language bindings have been deprecated in mpi 2.2 To disable this
warning use -Wno-deprecated.
src/mpi.cpp: In member function 'void MpiNode::report_MPI_ERROR(int)':
src/mpi.cpp:195: error: 'stderr' was not declared in this scope
src/mpi.cpp:195: error: 'fprintf' was not declared in this scope
make: *** [src/mpi.lo] Error 1
Compiling relion GUI ...
g++ -I/g/software/linux/pack/relion-1.2/SRC/relion-1.2/include
-I/usr/include/freetype2 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
-D_THREAD_SAFE -D_REENTRANT -o 'gui' 'gui.cpp'
/g/software/linux/pack/relion-1.2/SRC/relion-1.2/lib/libfltk.a -lXext
-lXft -lfontconfig -lXinerama -lpthread -ldl -lm -lX11
In file included from mainwindow.h:365,
from gui.cpp:23:
mainwindow.cpp: In member function 'void
RelionMainWindow::setupPreprocess()':
mainwindow.cpp:239: warning: deprecated conversion from string constant
to 'char*'
In file included from mainwindow.h:365,
from gui.cpp:23:
mainwindow.cpp: In member function 'void RelionMainWindow::setup(int,
bool)':
mainwindow.cpp:792: warning: deprecated conversion from string constant
to 'char*'
mainwindow.cpp:805: warning: deprecated conversion from string constant
to 'char*'
mainwindow.cpp:816: warning: deprecated conversion from string constant
to 'char*'
Done!
#
----------------
mpicc is version 4.4.6:
----------------
# $MPICXX --version
gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)
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.
#
----------------
The system is running CentOS 6 and the complete relion_build.log can be
found at http://pastebin.com/gnXA5baR. Relion builds fine with OpenMPI
but for several reasons it should be run with PMPI
Any ideas, why 'stderr' and 'fprintf' are "not declared in this scope"?
Cheers
frank
--
Frank Thommen - Structures IT Management and Support - EMBL Heidelberg
[log in to unmask] - +49 6221 387 8353
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