Cannot install, build error

[MikeDacre]

python setup.py build --slurm-lib=/usr/lib64/ --slurm-inc=/usr/include fails with the following error:

pyslurm/pyslurm.c: At top level:
pyslurm/pyslurm.c:68541:65: error: unknown type name ‘connection_type’
 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_connection_type(connection_type value) {
                                                             ^
pyslurm/pyslurm.c:68567:63: error: unknown type name ‘node_use_type’
 static CYTHON_INLINE PyObject* __Pyx_PyInt_From_node_use_type(node_use_type value) {
                                                               ^
error: command 'gcc' failed with exit status 1

System is CentOS 6.6 with the following packages:

slurm-devel-14.11.8-1.el6.x86_64
slurm-pam_slurm-14.11.8-1.el6.x86_64
slurm-plugins-14.11.8-1.el6.x86_64
slurm-torque-14.11.8-1.el6.x86_64
slurm-spank-x11-0.2.5-1.x86_64
slurm-perlapi-14.11.8-1.el6.x86_64
slurm-blcr-14.11.8-1.el6.x86_64
slurm-munge-14.11.8-1.el6.x86_64
slurm-14.11.8-1.el6.x86_64

rpm -ql slurm-devel | head -n 15 returns:

/usr/include/slurm
/usr/include/slurm/pmi.h
/usr/include/slurm/pmi2.h
/usr/include/slurm/slurm.h
/usr/include/slurm/slurm_errno.h
/usr/include/slurm/slurmdb.h
/usr/include/slurm/smd_ns.h
/usr/include/slurm/spank.h
/usr/lib64/libpmi.la
/usr/lib64/libpmi2.la
/usr/lib64/libslurm.la
/usr/lib64/libslurmdb.la
/usr/lib64/pkgconfig
/usr/lib64/pkgconfig/slurm.pc
/usr/share/man/man3/slurm_allocate_resources.3.gz

/usr/include/slurm/slurm.h includes the following lines:

enum node_use_type {
        SELECT_COPROCESSOR_MODE,/* use extra processor for communications */
        SELECT_VIRTUAL_NODE_MODE,/* application uses both processors */
        SELECT_NAV_MODE         /* either mode is acceptable */
};

enum connection_type {
        SELECT_MESH,            /* nodes wired in mesh */
        SELECT_TORUS,           /* nodes wired in torus */
        SELECT_NAV,             /* nodes wired in torus else mesh */
        SELECT_SMALL,           /* nodes in a small partition */
        SELECT_HTC_S,           /* nodes in a htc running SMP mode */
        SELECT_HTC_D,           /* nodes in a htc running Dual mode */
        SELECT_HTC_V,           /* nodes in a htc running VN mode */
        SELECT_HTC_L            /* nodes in a htc running in Linux mode */
};

I have no idea how to get it to install.

[gingergeeks]

Hi Mike,
I'm away from my test box at the moment but I can take a look tomorrow evening. I'm assuming this was with the 14.11.5 version of PySlurm you were using ?

You could try using - python setup.py build --slurm=/usr

Regards

Mark

[MikeDacre]

No problem. And it is the just a clone of the current git repo (as of two hours ago) that I am using. Using --slurm=/usr gives exactly the same error. I am not sure if it is unable to find the slurm.h file, or if there is something else missing.

[MikeDacre]

I just tried with the 14.11.5 branch and got a different error:

python setup.py build --slurm-lib=/usr/lib64 --slurm-inc=/usr/include
INFO:root:Info: 
INFO:root:Info: Building PySlurm (14.11.5)
INFO:root:Info: ------------------------------
INFO:root:Info: 
INFO:root:Info: Cython version 0.23.4 installed

INFO:root:Info: Clean - checking for objects to clean
INFO:root:Info: Clean - removing pyslurm build temp directory ...
INFO:root:Info: Clean - removing pyslurm/pyslurm.c temp file
INFO:root:Info: Clean - removing pyslurm/bluegene.pxi temp file
INFO:root:Info: Clean - completed
INFO:root:Info: Build - Detected Slurm include file version - 0x0e0b08 (14.11.08)
INFO:root:Info: Build - Writing Slurm version to pyslurm/slurm_version.pxi
INFO:root:Info: Build - Generating pyslurm/bluegene.pxi file
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/pyslurm
copying pyslurm/__init__.py -> build/lib.linux-x86_64-2.7/pyslurm
running build_ext
cythoning pyslurm/pyslurm.pyx to pyslurm/pyslurm.c
building 'pyslurm.pyslurm' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/pyslurm
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -I/usr/include -I/usr/include/slurm -fPIC -I/usr/include -I. -I/opt/rh/python27/root/usr/include/python2.7 -c pyslurm/pyslurm.c -o build/temp.linux-x86_64-2.7/pyslurm/pyslurm.o
{standard input}: Assembler messages:
{standard input}:1351: Error: expecting string instruction after `rep'
{standard input}:1356: Error: expecting string instruction after `rep'
error: command 'gcc' failed with exit status 1

[gingergeeks]

Mike,
Thank you for that trace. I'm now free for a month (Yay !) so I will have more free time. At first glance it looks like gcc is having an issue. What version of gcc are you using and what version of bin-utils are you using (as --version) ? The reason I ask is because I saw similar issues with an older version of binutils and after upgrading my errors went away.

Mark

[MikeDacre]

Yes, you were right. I changed the gcc build system on the server to a different version and it compiles fine now. I am having another issue now, but I will open a separate issue for that.

Thanks for your help.