Hello,
I'm trying to compile sage on a cluster with openmpi (distro:
slackware-current) and I'm getting the error below when trying to compile
pyzmq.
It seems that a '-R' option is passed to gcc, which makes the compiling
process fail. I tried a simple 'python setup.py build' in the
sage-6.9/local/var/tmp/sage/build/pyzmq-14.3.0/src directory and it
compiles fine, I have no idea where does this '-R' option come from.
Any hint would be very welcome.
Here is sage's log:
---------------------------
Found local metadata for pyzmq-14.3.0
Using cached file /usr/local/src/Math/sage-6.9/upstream/pyzmq-14.3.0.tar.gz
pyzmq-14.3.0
====================================================
Setting up build directory for pyzmq-14.3.0
Finished set up
****************************************************
Host system:
Linux helios 4.1.6 #2 SMP Fri Aug 21 01:28:50 CDT 2015 x86_64 Intel(R)
Xeon(R) CPU E5-2640 v3 @ 2.60GHz GenuineIntel GNU/Linux
****************************************************
C compiler: mpicc
C compiler version:
Reading specs from /usr/lib64/gcc/x86_64-slackware-linux/4.9.3/specs
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-slackware-linux/4.9.3/lto-wrapper
Target: x86_64-slackware-linux
Configured with: ../gcc-4.9.3/configure --prefix=/usr --libdir=/usr/lib64
--mandir=/usr/man --infodir=/usr/info --enable-shared --enable-bootstrap
--enable-languages=ada,c,c++,fortran,go,java,lto,objc
--enable-threads=posix --enable-checking=release --enable-objc-gc
--with-system-zlib --with-python-dir=/lib64/python2.7/site-packages
--disable-libunwind-exceptions --enable-__cxa_atexit --enable-libssp
--enable-lto --enable-install-libiberty --with-gnu-ld --verbose
--enable-java-home --with-java-home=/usr/lib64/jvm/jre
--with-jvm-root-dir=/usr/lib64/jvm
--with-jvm-jar-dir=/usr/lib64/jvm/jvm-exports --with-arch-directory=amd64
--with-antlr-jar=/root/slackware64-current/source/d/gcc/antlr-runtime-3.4.jar
--enable-java-awt=gtk --disable-gtktest --disable-multilib
--target=x86_64-slackware-linux --build=x86_64-slackware-linux
--host=x86_64-slackware-linux
Thread model: posix
gcc version 4.9.3 (GCC)
****************************************************
running configure
mpicc -DNDEBUG -g -fwrapv -O3 -Wall -O3 -march=native -fPIC
-I/usr/local/src/Math/sage-6.9/local/include -c
build/temp.linux-x86_64-2.7/scratch/check_sys_un.c -o
build/temp.linux-x86_64-2.7/scratch/check_sys_un.o
mpicc build/temp.linux-x86_64-2.7/scratch/check_sys_un.o
-L/usr/local/src/Math/sage-6.9/local/lib
-R/usr/local/src/Math/sage-6.9/local/lib -o
build/temp.linux-x86_64-2.7/scratch/check_sys_un
gcc: error: unrecognized command line option '-R'
Warning: No sys/un.h, IPC_PATH_MAX_LEN will be undefined: command 'mpicc'
failed with exit status 1
Configure: Autodetecting ZMQ settings...
Custom ZMQ dir: /usr/local/src/Math/sage-6.9/local
************************************************
creating build/temp.linux-x86_64-2.7/scratch/tmp
cc -c /tmp/timer_createjXOfUO.c -o
build/temp.linux-x86_64-2.7/scratch/tmp/timer_createjXOfUO.o
cc build/temp.linux-x86_64-2.7/scratch/tmp/timer_createjXOfUO.o -o
build/temp.linux-x86_64-2.7/scratch/a.out
build/temp.linux-x86_64-2.7/scratch/tmp/timer_createjXOfUO.o: In function
`main':
timer_createjXOfUO.c:(.text+0x15): undefined reference to `timer_create'
collect2: error: ld returned 1 exit status
mpicc -DNDEBUG -g -fwrapv -O3 -Wall -O3 -march=native -fPIC
-I/usr/local/src/Math/sage-6.9/local/include -Izmq/utils
-Izmq/backend/cython -Izmq/devices -c
build/temp.linux-x86_64-2.7/scratch/vers.c -o buil\
d/temp.linux-x86_64-2.7/scratch/vers.o
mpicc build/temp.linux-x86_64-2.7/scratch/vers.o
-L/usr/local/src/Math/sage-6.9/local/lib
-R/usr/local/src/Math/sage-6.9/local/lib -lzmq -lrt -o
build/temp.linux-x86_64-2.7/scratch/vers
gcc: error: unrecognized command line option '-R'
error: command 'mpicc' failed with exit status 1
Fatal: Falling back on bundled libzmq, but setup.cfg has explicitly
prohibited building the libzmq extension.
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