mvapich2-1.6 failed to build with PGI 10.0 on rhel6.1 system

Accelerated Computing HPC Compilers Legacy PGI Compilers
1

I have successfully built mvapich2-1.6 with PGI 10.0 on rhel 5.7 and rhel 4.9 systems.

But on rhel 6.1 system, the same build failed with following error:

CC topology-linux.lo
PGC-W-0221-Redefinition of symbol CPU_SET
(/usr/pgi/linux86-64/10.0/include/sched.h: 20)
PGC-W-0221-Redefinition of symbol CPU_CLR
(/usr/pgi/linux86-64/10.0/include/sched.h: 21)
PGC-W-0221-Redefinition of symbol CPU_ISSET
(/usr/pgi/linux86-64/10.0/include/sched.h: 22)
PGC-W-0221-Redefinition of symbol CPU_ZERO
(/usr/pgi/linux86-64/10.0/include/sched.h: 23)
PGC-S-0035-Syntax error: Recovery attempted by replacing identifier
sched_setaffinity by typedef id .Z0000 (topology-linux.c: 60)
PGC-S-0035-Syntax error: Recovery attempted by replacing identifier pid by
typedef id .Z0001 (topology-linux.c: 60)
PGC-S-0035-Syntax error: Recovery attempted by replacing identifier lg by
typedef id .Z0002 (topology-linux.c: 60)
PGC-S-0035-Syntax error: Recovery attempted by replacing identifier mask by
typedef id .Z0003 (topology-linux.c: 60)
PGC-W-0156-Type not specified, ‘int’ assumed (topology-linux.c: 60)
PGC-S-0035-Syntax error: Recovery attempted by replacing identifier
sched_getaffinity by typedef id .Z0004 (topology-linux.c: 93)
PGC-S-0035-Syntax error: Recovery attempted by replacing identifier pid by
typedef id .Z0005 (topology-linux.c: 93)
PGC-S-0035-Syntax error: Recovery attempted by replacing identifier lg by
typedef id .Z0006 (topology-linux.c: 93)
PGC-S-0035-Syntax error: Recovery attempted by replacing identifier mask by
typedef id .Z0007 (topology-linux.c: 93)
PGC-W-0156-Type not specified, ‘int’ assumed (topology-linux.c: 93)
PGC/x86-64 Linux 10.0-1: compilation completed with severe errors
make[8]: *** [topology-linux.lo] Error 1
make[8]: Leaving directory
`/usr/src/redhat/BUILD/mvapich2-1.6/src/mpid/ch3/channels/mrail/src/hwloc/src’
make[7]: *** [all-recursive] Error 1

Is this a known problem?
Does PGI have a fix for this?

Thank you for your help

Limin

2

Hi Limin,

We’re looking into it. Most likely there an incomparability with the system header files. I’ll let you know once we have better information.

  • Mat
3

Hi Mat,

Thank you for looking into this!

Limin

4

Hi Limin,

It looks like you just need to update your compiler version. PGI 2010 (10.x) only supports up to RHEL 5.0. We were able to build MVAPICH2-1.6 with the 11.8 compilers.

Best Regards,
Mat