Error while installing SLURM

[Monica Marathe]

Hello,

I am facing the following error while installing SLURM on my Fedora 20
machine.

/bin/sh ../../../../libtool --tag=CC --mode=link gcc -g -O2 -pthread
-fno-gcse -module -avoid-version --export-dynamic -Wl,-rpath
-Wl,/usr/lib64 -L/usr/lib64 -o auth_munge.la -rpath /usr/lib/slurm
auth_munge.lo -lmunge
libtool: link: gcc -shared -fPIC -DPIC .libs/auth_munge.o -L/usr/lib64
-lmunge -O2 -pthread -Wl,-rpath -Wl,/usr/lib64 -pthread -Wl,-soname
-Wl,auth_munge.so -o .libs/auth_munge.so
/usr/bin/ld: skipping incompatible
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.so when searching
for -lmunge
/usr/bin/ld:
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.a(ctx.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a
shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.a: could not read
symbols: Bad value
collect2: error: ld returned 1 exit status
make[5]: *** [auth_munge.la] Error 1
make[5]: Leaving directory
`/home/Monica/slurm-14.03.7/src/plugins/auth/munge'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins/auth'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Monica/slurm-14.03.7/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/Monica/slurm-14.03.7'
make: *** [all] Error 2

I tried to install using the command:
./configure --prefix=/usr --sysconfdir=/etc --localstatedir=/var && make &&
make install

Please tell me how to fix this.

Regards,
Monica

[Jared David Baker]

Monica,

The Slurm build is trying to make a shared library and link against munge (which you can see from the output below). It seems that the linker finds an incompatible libmunge.so when trying to perform the link, skips it for incompatibility, and tries to link against the static library which has not been compiled for position independent code (as many static libraries are not compiled that way) and therefore it cannot read the symbols. So my question to you would be if this is a Fedora 20 machine, how did you install munge?

I only ask because you seem to have some redhat stuff in paths below and the rpms might not be quite compatible.

Best,

Jared

From: Monica Marathe [mailto:***@gmail.com]
Sent: Monday, September 22, 2014 3:05 PM
To: slurm-dev
Subject: [slurm-dev] Error while installing SLURM

Hello,
I am facing the following error while installing SLURM on my Fedora 20 machine.

/bin/sh ../../../../libtool --tag=CC --mode=link gcc -g -O2 -pthread -fno-gcse -module -avoid-version --export-dynamic -Wl,-rpath -Wl,/usr/lib64 -L/usr/lib64 -o auth_munge.la<http://auth_munge.la> -rpath /usr/lib/slurm auth_munge.lo -lmunge
libtool: link: gcc -shared -fPIC -DPIC .libs/auth_munge.o -L/usr/lib64 -lmunge -O2 -pthread -Wl,-rpath -Wl,/usr/lib64 -pthread -Wl,-soname -Wl,auth_munge.so -o .libs/auth_munge.so
/usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.so when searching for -lmunge
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.a(ctx.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[5]: *** [auth_munge.la<http://auth_munge.la>] Error 1
make[5]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins/auth/munge'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins/auth'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Monica/slurm-14.03.7/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/Monica/slurm-14.03.7'
make: *** [all] Error 2
I tried to install using the command:
./configure --prefix=/usr --sysconfdir=/etc --localstatedir=/var && make && make install

Please tell me how to fix this.
Regards,
Monica

[Monica Marathe]

Hi Jared,

http://koji.fedoraproject.org/koji/buildinfo?buildID=460466

This is the site from where I've installed the munge rpms. Does SLURM come
packaged for Fedora 20 with munge integrated?

Regards,
Monica

Post by Jared David Baker
Monica,
The Slurm build is trying to make a shared library and link against munge
(which you can see from the output below). It seems that the linker finds
an incompatible libmunge.so when trying to perform the link, skips it for
incompatibility, and tries to link against the static library which has not
been compiled for position independent code (as many static libraries are
not compiled that way) and therefore it cannot read the symbols. So my
question to you would be if this is a Fedora 20 machine, how did you
install munge?
I only ask because you seem to have some redhat stuff in paths below and
the rpms might not be quite compatible.
Best,
Jared
*Sent:* Monday, September 22, 2014 3:05 PM
*To:* slurm-dev
*Subject:* [slurm-dev] Error while installing SLURM
Hello,
I am facing the following error while installing SLURM on my Fedora 20 machine.
/bin/sh ../../../../libtool --tag=CC --mode=link gcc -g -O2 -pthread
-fno-gcse -module -avoid-version --export-dynamic -Wl,-rpath
-Wl,/usr/lib64 -L/usr/lib64 -o auth_munge.la -rpath /usr/lib/slurm
auth_munge.lo -lmunge
libtool: link: gcc -shared -fPIC -DPIC .libs/auth_munge.o -L/usr/lib64
-lmunge -O2 -pthread -Wl,-rpath -Wl,/usr/lib64 -pthread -Wl,-soname
-Wl,auth_munge.so -o .libs/auth_munge.so
/usr/bin/ld: skipping incompatible
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.so when searching
for -lmunge
relocation R_X86_64_32S against `.rodata' can not be used when making a
shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.a: could not read
symbols: Bad value
collect2: error: ld returned 1 exit status
make[5]: *** [auth_munge.la] Error 1
make[5]: Leaving directory
`/home/Monica/slurm-14.03.7/src/plugins/auth/munge'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins/auth'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Monica/slurm-14.03.7/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/Monica/slurm-14.03.7'
make: *** [all] Error 2
./configure --prefix=/usr --sysconfdir=/etc --localstatedir=/var && make && make install
Please tell me how to fix this.
Regards,
Monica
--
- Monica Marathe
[image: Image removed by sender.]

[Michael Jennings]

Monica,

What's happening here is that you're building a 64-bit SLURM, but either
you only have 32-bit munge installed, or that's the only one it's finding.
The "skipping incompatible" message is telling you it found
/usr/lib/libmunge.so but ignored it because it's 32-bit and you're building
64-bit SLURM.

Make sure you have munge-devel.x86_64 installed, or build 32-bit SLURM
instead. Either one should resolve the issue you're seeing.

HTH,
Michael

Post by Monica Marathe
Hi Jared,
http://koji.fedoraproject.org/koji/buildinfo?buildID=460466
This is the site from where I've installed the munge rpms. Does SLURM come
packaged for Fedora 20 with munge integrated?
Regards,
Monica

Post by Jared David Baker
Monica,
The Slurm build is trying to make a shared library and link against munge
(which you can see from the output below). It seems that the linker finds
an incompatible libmunge.so when trying to perform the link, skips it for
incompatibility, and tries to link against the static library which has not
been compiled for position independent code (as many static libraries are
not compiled that way) and therefore it cannot read the symbols. So my
question to you would be if this is a Fedora 20 machine, how did you
install munge?
I only ask because you seem to have some redhat stuff in paths below and
the rpms might not be quite compatible.
Best,
Jared
*Sent:* Monday, September 22, 2014 3:05 PM
*To:* slurm-dev
*Subject:* [slurm-dev] Error while installing SLURM
Hello,
I am facing the following error while installing SLURM on my Fedora 20 machine.
/bin/sh ../../../../libtool --tag=CC --mode=link gcc -g -O2 -pthread
-fno-gcse -module -avoid-version --export-dynamic -Wl,-rpath
-Wl,/usr/lib64 -L/usr/lib64 -o auth_munge.la -rpath /usr/lib/slurm
auth_munge.lo -lmunge
libtool: link: gcc -shared -fPIC -DPIC .libs/auth_munge.o
-L/usr/lib64 -lmunge -O2 -pthread -Wl,-rpath -Wl,/usr/lib64 -pthread
-Wl,-soname -Wl,auth_munge.so -o .libs/auth_munge.so
/usr/bin/ld: skipping incompatible
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.so when searching
for -lmunge
relocation R_X86_64_32S against `.rodata' can not be used when making a
shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.a: could not
read symbols: Bad value
collect2: error: ld returned 1 exit status
make[5]: *** [auth_munge.la] Error 1
make[5]: Leaving directory
`/home/Monica/slurm-14.03.7/src/plugins/auth/munge'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins/auth'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Monica/slurm-14.03.7/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/Monica/slurm-14.03.7'
make: *** [all] Error 2
./configure --prefix=/usr --sysconfdir=/etc --localstatedir=/var && make && make install
Please tell me how to fix this.
Regards,
Monica
--
- Monica Marathe
[image: Image removed by sender.]

--
- Monica Marathe

[Monica Marathe]

Hi Michael,

Thanks so much for your suggestion. I reinstalled munge-devel.x86_64 and
that seems to have taken care of the error. However when i make and make
install now, it gives me the following error:

/bin/sh ../../libtool --mode=install /usr/bin/install -c libslurm.la
libpmi.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libslurm.so.27.0.0
/usr/local/lib/libslurm.so.27.0.0
/usr/bin/install: cannot remove '/usr/local/lib/libslurm.so.27.0.0':
Permission denied
make[4]: *** [install-libLTLIBRARIES] Error 1
make[4]: Leaving directory `/home/Monica/slurm-14.03.7/src/api'
make[3]: *** [install-am] Error 2
make[3]: Leaving directory `/home/Monica/slurm-14.03.7/src/api'
make[2]: *** [install] Error 2
make[2]: Leaving directory `/home/Monica/slurm-14.03.7/src/api'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/Monica/slurm-14.03.7/src'
make: *** [install-recursive] Error 1

Any suggestions on what the problem could be?

Thanks and Regards,
Monica

Post by Jared David Baker
Monica,
What's happening here is that you're building a 64-bit SLURM, but either
you only have 32-bit munge installed, or that's the only one it's finding.
The "skipping incompatible" message is telling you it found
/usr/lib/libmunge.so but ignored it because it's 32-bit and you're building
64-bit SLURM.
Make sure you have munge-devel.x86_64 installed, or build 32-bit SLURM
instead. Either one should resolve the issue you're seeing.
HTH,
Michael

Post by Monica Marathe
Hi Jared,
http://koji.fedoraproject.org/koji/buildinfo?buildID=460466
This is the site from where I've installed the munge rpms. Does SLURM
come packaged for Fedora 20 with munge integrated?
Regards,
Monica

Post by Jared David Baker
Monica,
The Slurm build is trying to make a shared library and link against
munge (which you can see from the output below). It seems that the linker
finds an incompatible libmunge.so when trying to perform the link, skips it
for incompatibility, and tries to link against the static library which has
not been compiled for position independent code (as many static libraries
are not compiled that way) and therefore it cannot read the symbols. So my
question to you would be if this is a Fedora 20 machine, how did you
install munge?
I only ask because you seem to have some redhat stuff in paths below and
the rpms might not be quite compatible.
Best,
Jared
*Sent:* Monday, September 22, 2014 3:05 PM
*To:* slurm-dev
*Subject:* [slurm-dev] Error while installing SLURM
Hello,
I am facing the following error while installing SLURM on my Fedora 20 machine.
/bin/sh ../../../../libtool --tag=CC --mode=link gcc -g -O2 -pthread
-fno-gcse -module -avoid-version --export-dynamic -Wl,-rpath
-Wl,/usr/lib64 -L/usr/lib64 -o auth_munge.la -rpath /usr/lib/slurm
auth_munge.lo -lmunge
libtool: link: gcc -shared -fPIC -DPIC .libs/auth_munge.o
-L/usr/lib64 -lmunge -O2 -pthread -Wl,-rpath -Wl,/usr/lib64 -pthread
-Wl,-soname -Wl,auth_munge.so -o .libs/auth_munge.so
/usr/bin/ld: skipping incompatible
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.so when searching
for -lmunge
relocation R_X86_64_32S against `.rodata' can not be used when making a
shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../libmunge.a: could not
read symbols: Bad value
collect2: error: ld returned 1 exit status
make[5]: *** [auth_munge.la] Error 1
make[5]: Leaving directory
`/home/Monica/slurm-14.03.7/src/plugins/auth/munge'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins/auth'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/Monica/slurm-14.03.7/src/plugins'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Monica/slurm-14.03.7/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/Monica/slurm-14.03.7'
make: *** [all] Error 2
./configure --prefix=/usr --sysconfdir=/etc --localstatedir=/var && make
&& make install
Please tell me how to fix this.
Regards,
Monica
--
- Monica Marathe
[image: Image removed by sender.]

--
- Monica Marathe

--
Senior HPC Systems Engineer
High-Performance Computing Services
Lawrence Berkeley National Laboratory
Bldg 50B-3209E W: 510-495-2687
MS 050B-3209 F: 510-486-8615

[Michael Jennings]

Post by Monica Marathe
/bin/sh ../../libtool --mode=install /usr/bin/install -c libslurm.la
libpmi.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libslurm.so.27.0.0
/usr/local/lib/libslurm.so.27.0.0
Permission denied

Monica,

Here's the actual error. Your current user doesn't have write access to
/usr/local/lib. Are you running as root? Perhaps you need "sudo make
install" instead of just "make install" or something similar? Or is
/usr/local perhaps mounted with root_squash?

Michael

[Monica Marathe]

Hi Michael,

Yep, I acquired root privileges and am now able to install it.

Thanks for you help!

-Monica

On Tue, Sep 23, 2014 at 10:50 AM, Monica Marathe <

Post by Monica Marathe
/bin/sh ../../libtool --mode=install /usr/bin/install -c libslurm.la
libpmi.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libslurm.so.27.0.0
/usr/local/lib/libslurm.so.27.0.0
Permission denied

Monica,
Here's the actual error. Your current user doesn't have write access to
/usr/local/lib. Are you running as root? Perhaps you need "sudo make
install" instead of just "make install" or something similar? Or is
/usr/local perhaps mounted with root_squash?
Michael
--
Senior HPC Systems Engineer
High-Performance Computing Services
Lawrence Berkeley National Laboratory
Bldg 50B-3209E W: 510-495-2687
MS 050B-3209 F: 510-486-8615