compilation of gaussian03

I just tried to install gaussian03 on FC4, using PGI Workstation 6.0, but goe the error information:
util.so: undefined reference to `pthread_kill_other_threads_np’.

My system using NPTL 2.3.5. Could anybody tell me how to deal with this problem?

Thanks

Sincerely

Aihua

I have commented out the “#pthread_kill_other_threads_np()” line in mdutil.c file, and the installation went on. But there are other errors occurring:

ml0.o(.text+0x2c5): In function ml0': /scratch/g03/ml0.f:114: undefined reference to gauabt_’
ml0.o(.text+0x359):/scratch/g03/ml0.f:117: undefined reference to gauabt_' ml0.o(.text+0x431):/scratch/g03/ml0.f:122: undefined reference to gauabt_’
ml0.o(.text+0x517):/scratch/g03/ml0.f:128: undefined reference to gauabt_' ml0.o(.text+0x671):/scratch/g03/ml0.f:139: undefined reference to gauabt_’
ml0.o(.text+0x694):/scratch/g03/ml0.f:142: undefined reference to fixinout_' ml0.o(.text+0xef1):/scratch/g03/ml0.f:208: undefined reference to ggeten_’
ml0.o(.text+0xfd7):/scratch/g03/ml0.f:216: undefined reference to getexen_' ml0.o(.text+0x127e):/scratch/g03/ml0.f:231: undefined reference to gaufls_’
ml0.o(.text+0x1294):/scratch/g03/ml0.f:236: undefined reference to gsyst_' util.so: undefined reference to writwa_’
util.so: undefined reference to closwa_' util.so: undefined reference to asynwa_’
util.so: undefined reference to erfcx_' util.so: undefined reference to fixstdin_’
util.so: undefined reference to fixenv_' util.so: undefined reference to ifalph_’
util.so: undefined reference to ntrsiz_' util.so: undefined reference to guname_’
util.so: undefined reference to openwa_' util.so: undefined reference to envfil_’
util.so: undefined reference to gfree_' util.so: undefined reference to gauexec_’
util.so: undefined reference to readwa_' util.so: undefined reference to machin_’
util.so: undefined reference to galloc_' util.so: undefined reference to ntrbks_’
util.so: undefined reference to appfpd_' util.so: undefined reference to gfree1_’
util.so: undefined reference to waitwa_' util.so: undefined reference to ntrext1_’
util.so: undefined reference to intchr_' util.so: undefined reference to getscm_’
util.so: undefined reference to gsr48_' util.so: undefined reference to setcore_’
util.so: undefined reference to galloc1_' util.so: undefined reference to drand48_’
util.so: undefined reference to gtrap_' util.so: undefined reference to appfp_’
make: *** [g03] Error 2

Does anybody know why?

Hi Aihua,

We had another user (see post #267) who had runtime problems on Fedora Core 4, but this implies he was able to get it built. Unfortunately, we have not seen this error nor know how to fix it. You should contact Gaussian directly and see if they can help. I do know that they don’t support Fedora Core 4 yet, but this might be a more general issue.

  • Mat

The thing is to install Gaussian03 on Suse 10.1
Compiler 6.2

When compiling it stops with this error:

util.so: undefined reference to `pthread_kill_other_threads_np’

Any ideas?

Thanks, Marcelo.

Hi Marcelo,

While I can’t verify nor recommend the following solution, searching the web I found the following on Fedora Forum.

Since kernel 2.6 is NPTL the function pthread_kill_other_threads_np() is no longer available. It was used to ensure POSIX exec(). This is no longer needed under the new threading library so just comment it out. Line 1268 of bsd/mdutil.c

However, I would encourage you to contact Gaussian directly and see if they have a fix for this issue.

Hope this helps,
Mat

Thank you Mat.
I have tryied that, but there are other problems, also reported in the net before and with no apparent solutions. However Gaussian claims their software is compatible with Suse 10.1, but they are not telling me yet anything abot how to make it work.

Marcelo.

Could you send the last compile command, please?

As the undefined references seem to be in mdutil.c, I guess you should link with mdutil.o which might be in bsd/mdutil.o.