compiling vasp error; opteron; fedora 4

[jrgomes]

pgf90 -o vasp -tp k8-64 main.o base.o mpi.o smart_allocate.o xml.o constant.o jacobi.o main_mpi.o scala.o asa.o lattice.o poscar.o ini.o setex.o radial.o pseudo.o mgrid.o mkpoints.o wave.o wave_mpi.o symmetry.o symlib.o lattlib.o random.o nonl.o nonlr.o dfast.o choleski2.o mix.o charge.o xcgrad.o xcspin.o potex1.o potex2.o metagga.o constrmag.o pot.o cl_shift.o force.o dos.o elf.o tet.o hamil.o steep.o chain.o dyna.o relativistic.o LDApU.o sphpro.o paw.o us.o ebs.o wavpre.o wavpre_noio.o broyden.o dynbr.o rmm-diis.o reader.o writer.o tutor.o xml_writer.o brent.o stufak.o fileio.o opergrid.o stepver.o dipol.o xclib.o chgloc.o subrot.o optreal.o davidson.o edtest.o electron.o shm.o pardens.o paircorrection.o optics.o constr_cell_relax.o stm.o finite_diff.o elpol.o setlocalpp.o fftw3d.o fft3dlib.o ../fftw-3.0.1/.libs/libfftw3.a -L../vasp.4.lib -ldmy ../vasp.4.lib/linpack_double.o ../vasp.4.lib/lapack_double.o /libgoto_opteron64p-r1.00.so
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in main.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in main.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in main.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in poscar.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in ini.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in ini.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in radial.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in symmetry.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in nonl.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in nonlr.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in constrmag.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in constrmag.o
/usr/bin/ld: Warning: alignment 16 of symbol `cl_5_' in cl_shift.o is smaller than 32 in main.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in cl_shift.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in chain.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in dyna.o
/usr/bin/ld: Warning: alignment 16 of symbol `ldaplusu_module_5_' in LDApU.o is smaller than 32 in main.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in LDApU.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in LDApU.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in LDApU.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in LDApU.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in sphpro.o
/usr/bin/ld: Warning: alignment 16 of symbol `paw_2_' in paw.o is smaller than 32 in main.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in paw.o
/usr/bin/ld: Warning: alignment 16 of symbol `cl_5_' in cl_shift.o is smaller than 32 in paw.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in paw.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in paw.o
/usr/bin/ld: Warning: alignment 16 of symbol `ldaplusu_module_5_' in LDApU.o is smaller than 32 in paw.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in us.o
/usr/bin/ld: Warning: alignment 16 of symbol `paw_2_' in paw.o is smaller than 32 in us.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in dynbr.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in reader.o/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in reader.o/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in writer.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in writer.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in writer.o/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in writer.o/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in xml_writer.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in xml_writer.o
/usr/bin/ld: Warning: alignment 16 of symbol `paw_2_' in paw.o is smaller than 32 in fileio.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in dipol.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in dipol.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in subrot.o
/usr/bin/ld: Warning: alignment 16 of symbol `paw_2_' in paw.o is smaller than 32 in electron.o
/usr/bin/ld: Warning: alignment 16 of symbol `cl_5_' in cl_shift.o is smaller than 32 in electron.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_2_' in xml.o is smaller than 32 in electron.o
/usr/bin/ld: Warning: alignment 16 of symbol `vaspxml_1_' in xml.o is smaller than 32 in electron.o
/usr/bin/ld: Warning: alignment 16 of symbol `ldaplusu_module_5_' in LDApU.o is smaller than 32 in electron.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in shm.o
/usr/bin/ld: Warning: alignment 16 of symbol `asa_2_' in asa.o is smaller than 32 in elpol.o
/usr/bin/ld: Warning: alignment 16 of symbol `main_mpi_2_' in main_mpi.o is smaller than 32 in elpol.o
/usr/bin/ld: Warning: alignment 16 of symbol `paw_2_' in paw.o is smaller than 32 in elpol.o
/libgoto_opteron64p-r1.00.so: undefined reference to `pthread_create'
/libgoto_opteron64p-r1.00.so: undefined reference to `pthread_join'

Machine: opteron with Fedora 4 (2.6.11-1.1369_FC4smp)
Any idea?

Thanks in advance

[jrgomes]

I've forget to tell that I was able to compile VASP on the same machine with the ATLAS/BLAS libraries. Thus, the problem maybe related with the use of the libgoto_opteron64p-r1.00.so library.

[job]

GOTO BLAS requires the pthread libraries. Add '-lpthread' to your LIB flags (after libgoto).
<span class='smallblacktext'>[ Edited Mon Dec 19 2005, 10:46AM ]</span>

[jrgomes]

Thanks! The program is now compiled, however, the warnings still appear. Anybody knows if it causes any kind of problems in serial/parallel execution of VASP?

All the best

[job]

Perhaps you're compiling with too little optimization. Try the '-Mcache_align' flag. '-fast' might also help, if you weren't using it before.

Also, for the MPI version of VASP using GOTO BLAS, you might want to set the GOTO_NUM_THREADS environment variable to 1.
<span class='smallblacktext'>[ Edited Wed Dec 28 2005, 02:53PM ]</span>

[jrgomes]

With the extra optimization flags the warnings still appear. Probably this is due to the newest linux versions that do not include g77 by default and include a mixture of gcc_3xx and gcc_4xx packages.

[admin]

the alignment errors are most probably due to specifying the wrong
(ie 32-bit) processor type (-tp in OFLAGS) for a 64-bit processor and compiler