Cannot compile singularity with -pg flag

[renganxu]

Version of Singularity:

2.4.2

Expected behavior

Singularity should be built successfully with -pg flag.

Actual behavior

...
gcc -DHAVE_CONFIG_H -I. -DBINDIR="/cm/shared/apps/singularity/dev/bin" -DSYSCONFDIR="/cm/shared/apps/singulari
ty/dev/etc" -DLOCALSTATEDIR="/cm/shared/apps/singularity/dev/var" -DLIBEXECDIR="/cm/shared/apps/singularity/de
v/libexec" -DNS_CLONE_NEWPID -DNS_CLONE_FS -DNS_CLONE_NEWNS -DNS_CLONE_NEWUSER -DNS_CLONE_NEWIPC -DNS_CLONE_NEWNET -DSINGULARITY_NO_NEW_PRIVS -DSINGULARITY_MS_SLAVE -Wall -fpie -fPIC -g -pg -O2 -MT util/action-mount.o -MD -MP -MF util/.deps/action-mount.Tpo -c -o util/action-mount.o test -f 'util/mount.c' || echo './'util/mount.c
mv -f util/.deps/action-mount.Tpo util/.deps/action-mount.Po

/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -fpie -fPIC -g -pg -O2 -pie -pg -Wl,-rpath -Wl,/cm/shared/apps/singularity/dev/lib -o action action-action.o util/action-util.o util/action-file.o util/action-registry.o util/action-privilege.o util/action-sessiondir.o util/action-suid.o util/action-cleanupd.o util/action-daemon.o util/action-mount.o lib/image/libsingularity-image.la lib/runtime/libsingularity-runtime.la action-lib/libinternal.la

libtool: link: gcc -Wall -fpie -fPIC -g -pg -O2 -pie -pg -Wl,-rpath -Wl,/cm/shared/apps/singularity/dev/lib -o .libs/action action-action.o util/action-util.o util/action-file.o util/action-registry.o util/action-privilege.o util/action-sessiondir.o util/action-suid.o util/action-cleanupd.o util/action-daemon.o util/action-mount.o lib/image/.libs/libsingularity-image.so lib/runtime/.libs/libsingularity-runtime.so action-lib/.libs/libinternal.a -Wl,-rpath -Wl,/cm/shared/apps/singularity/dev/lib/singularity

/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/gcrt1.o: relocation R_X86_64_32S against `__libc_csu_fini' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/gcrt1.o: could not read symbols: Bad value
collect2: error: ld returned 1 exit status

Steps to reproduce behavior

$ cd singularity-2.4.2
$ ./autogen.sh
$ ./configure --prefix=/cm/shared/apps/singularity/dev
change the following two lines in Makefile, src/Makefile and src/lib/Makefile
CFLAGS = -g -O2
LDFLAGS = -Wl,-rpath -Wl,$(libdir)
to
CFLAGS = -g -pg -O2
LDFLAGS = -pg -Wl,-rpath -Wl,$(libdir)

$ make

Background:

My MPI program which was built in and run with Singularity container has very poor performance compared to the bare-metal one (~2x slower). I ran the MPI program on 8 nodes to make their difference more obvious. My host OS is RHEL 7.3 and Singularity OS is Centos 7.4. I have two copies of MPI program binaries. One copy was compiled on the host/bare-metal, and another copy was compiled in container. Now the one compiled in container has very poor performance when running with the container, but the its performance is normal if running on the host. So I think it's the problem of the container.

Now I want to profile Singularity to see which function caused the problem. My MPI program is also a GPU program and Nvidia's profile nvprof cannot profile CPU part in MPI program. So I have to profile Singularity with GPROF tool which requires Singularity to build with -pg flag.

Regards,
Rengan

[jscook2345]

@hfutxrg

With the release of 3.0 a lot of Singularity was rewritten in Go. There is still some C, but perhaps you could try the new release and let us know how things work out? Please let me know if you have further questions!

[GodloveD]

I'm going to assume this is no longer relevant. Please request it to be re-opened if I'm wrong. Thank you!