compiling vasp error; opteron; fedora 4

Questions regarding the compilation of VASP on various platforms: hardware, compilers and libraries, etc.


Moderators: Global Moderator, Moderator

Post Reply
Message
Author
jrgomes
Newbie
Newbie
Posts: 4
Joined: Wed Oct 13, 2004 9:10 am
License Nr.: 52-paw

compiling vasp error; opteron; fedora 4

#1 Post by jrgomes » Mon Dec 12, 2005 7:38 pm

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 vaspxml1_′∈xml.oissmal≤rthan32∈ma∈.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_2_' in xml.o is smaller than 32 in main.o
/usr/bin/ld: Warning: alignment 16 of symbol ma∈mπ2_′∈ma∈mπ.oissmal≤rthan32∈ma∈.ousrb∈ld:Warn∈g:alignment16ofsymbolmain_mpi_2_' in main_mpi.o is smaller than 32 in poscar.o
/usr/bin/ld: Warning: alignment 16 of symbol vaspxml2_′∈xml.oissmal≤rthan32∈∈i.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_1_' in xml.o is smaller than 32 in ini.o
/usr/bin/ld: Warning: alignment 16 of symbol asa2_′∈asa.oissmal≤rthan32∈radial.ousrb∈ld:Warn∈g:alignment16ofsymbolmain_mpi_2_' in main_mpi.o is smaller than 32 in symmetry.o
/usr/bin/ld: Warning: alignment 16 of symbol asa2_′∈asa.oissmal≤rthan32∈nonl.ousrb∈ld:Warn∈g:alignment16ofsymbolasa_2_' in asa.o is smaller than 32 in nonlr.o
/usr/bin/ld: Warning: alignment 16 of symbol vaspxml2_′∈xml.oissmal≤rthan32∈constrmag.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_1_' in xml.o is smaller than 32 in constrmag.o
/usr/bin/ld: Warning: alignment 16 of symbol cl5_′∈clshift.oissmal≤rthan32∈ma∈.ousrb∈ld:Warn∈g:alignment16ofsymbolasa_2_' in asa.o is smaller than 32 in cl_shift.o
/usr/bin/ld: Warning: alignment 16 of symbol ma∈mπ2_′∈ma∈mπ.oissmal≤rthan32∈cha∈.ousrb∈ld:Warn∈g:alignment16ofsymbolmain_mpi_2_' in main_mpi.o is smaller than 32 in dyna.o
/usr/bin/ld: Warning: alignment 16 of symbol ldaplusumode̲5_′∈LDApU.oissmal≤rthan32∈ma∈.ousrb∈ld:Warn∈g:alignment16ofsymbolmain_mpi_2_' in main_mpi.o is smaller than 32 in LDApU.o
/usr/bin/ld: Warning: alignment 16 of symbol asa2_′∈asa.oissmal≤rthan32∈LDApU.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_2_' in xml.o is smaller than 32 in LDApU.o
/usr/bin/ld: Warning: alignment 16 of symbol vaspxml1_′∈xml.oissmal≤rthan32∈LDApU.ousrb∈ld:Warn∈g:alignment16ofsymbolmain_mpi_2_' in main_mpi.o is smaller than 32 in sphpro.o
/usr/bin/ld: Warning: alignment 16 of symbol paw2_′∈paw.oissmal≤rthan32∈ma∈.ousrb∈ld:Warn∈g:alignment16ofsymbolasa_2_' in asa.o is smaller than 32 in paw.o
/usr/bin/ld: Warning: alignment 16 of symbol cl5_′∈clshift.oissmal≤rthan32∈paw.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_2_' in xml.o is smaller than 32 in paw.o
/usr/bin/ld: Warning: alignment 16 of symbol vaspxml1_′∈xml.oissmal≤rthan32∈paw.ousrb∈ld:Warn∈g:alignment16ofsymbolldaplusu_module_5_' in LDApU.o is smaller than 32 in paw.o
/usr/bin/ld: Warning: alignment 16 of symbol asa2_′∈asa.oissmal≤rthan32∈us.ousrb∈ld:Warn∈g:alignment16ofsymbolpaw_2_' in paw.o is smaller than 32 in us.o
/usr/bin/ld: Warning: alignment 16 of symbol ma∈mπ2_′∈ma∈mπ.oissmal≤rthan32∈dynbr.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_2_' in xml.o is smaller than 32 in reader.o/usr/bin/ld: Warning: alignment 16 of symbol vaspxml1_′∈xml.oissmal≤rthan32∈reader.ousrb∈ld:Warn∈g:alignment16ofsymbolmain_mpi_2_' in main_mpi.o is smaller than 32 in writer.o
/usr/bin/ld: Warning: alignment 16 of symbol asa2_′∈asa.oissmal≤rthan32∈writer.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_2_' in xml.o is smaller than 32 in writer.o/usr/bin/ld: Warning: alignment 16 of symbol vaspxml1_′∈xml.oissmal≤rthan32∈writer.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_2_' in xml.o is smaller than 32 in xml_writer.o
/usr/bin/ld: Warning: alignment 16 of symbol vaspxml1_′∈xml.oissmal≤rthan32∈xmlwriter.ousrb∈ld:Warn∈g:alignment16ofsymbolpaw_2_' in paw.o is smaller than 32 in fileio.o
/usr/bin/ld: Warning: alignment 16 of symbol vaspxml2_′∈xml.oissmal≤rthan32∈dipol.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_1_' in xml.o is smaller than 32 in dipol.o
/usr/bin/ld: Warning: alignment 16 of symbol ma∈mπ2_′∈ma∈mπ.oissmal≤rthan32∈⊂rot.ousrb∈ld:Warn∈g:alignment16ofsymbolpaw_2_' in paw.o is smaller than 32 in electron.o
/usr/bin/ld: Warning: alignment 16 of symbol cl5_′∈clshift.oissmal≤rthan32∈e≤ctron.ousrb∈ld:Warn∈g:alignment16ofsymbolvaspxml_2_' in xml.o is smaller than 32 in electron.o
/usr/bin/ld: Warning: alignment 16 of symbol vaspxml1_′∈xml.oissmal≤rthan32∈e≤ctron.ousrb∈ld:Warn∈g:alignment16ofsymbolldaplusu_module_5_' in LDApU.o is smaller than 32 in electron.o
/usr/bin/ld: Warning: alignment 16 of symbol ma∈mπ2_′∈ma∈mπ.oissmal≤rthan32∈shm.ousrb∈ld:Warn∈g:alignment16ofsymbolasa_2_' in asa.o is smaller than 32 in elpol.o
/usr/bin/ld: Warning: alignment 16 of symbol ma∈mπ2_′∈ma∈mπ.oissmal≤rthan32∈elpol.ousrb∈ld:Warn∈g:alignment16ofsymbolpaw_2_' in paw.o is smaller than 32 in elpol.o
/libgoto_opteron64p-r1.00.so: undefined reference to pthreadcreate′libgo→opteron64p-r1.00.so:undef∈edreference→pthread_join'

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

Thanks in advance
Last edited by jrgomes on Mon Dec 12, 2005 7:38 pm, edited 1 time in total.
Top
jrgomes
Newbie
Newbie
Posts: 4
Joined: Wed Oct 13, 2004 9:10 am
License Nr.: 52-paw

compiling vasp error; opteron; fedora 4

#2 Post by jrgomes » Fri Dec 16, 2005 4:04 pm

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.
Last edited by jrgomes on Fri Dec 16, 2005 4:04 pm, edited 1 time in total.
Top
job
Jr. Member
Jr. Member
Posts: 55
Joined: Tue Aug 16, 2005 7:44 am

compiling vasp error; opteron; fedora 4

#3 Post by job » Mon Dec 19, 2005 9:44 am

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>
Last edited by job on Mon Dec 19, 2005 9:44 am, edited 1 time in total.
Top
jrgomes
Newbie
Newbie
Posts: 4
Joined: Wed Oct 13, 2004 9:10 am
License Nr.: 52-paw

compiling vasp error; opteron; fedora 4

#4 Post by jrgomes » Thu Dec 22, 2005 6:44 pm

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
Last edited by jrgomes on Thu Dec 22, 2005 6:44 pm, edited 1 time in total.
Top
job
Jr. Member
Jr. Member
Posts: 55
Joined: Tue Aug 16, 2005 7:44 am

compiling vasp error; opteron; fedora 4

#5 Post by job » Wed Dec 28, 2005 1:50 pm

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>
Last edited by job on Wed Dec 28, 2005 1:50 pm, edited 1 time in total.
Top
jrgomes
Newbie
Newbie
Posts: 4
Joined: Wed Oct 13, 2004 9:10 am
License Nr.: 52-paw

compiling vasp error; opteron; fedora 4

#6 Post by jrgomes » Fri Jan 06, 2006 10:32 am

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.
Last edited by jrgomes on Fri Jan 06, 2006 10:32 am, edited 1 time in total.
Top
admin
Administrator
Administrator
Posts: 2921
Joined: Tue Aug 03, 2004 8:18 am
License Nr.: 458

compiling vasp error; opteron; fedora 4

#7 Post by admin » Wed Oct 04, 2006 1:10 pm

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
Last edited by admin on Wed Oct 04, 2006 1:10 pm, edited 1 time in total.
Top
Post Reply

Return to “Installation issues”