Dear AMBERs,
Just wanted to let you know that the error 'final link failed' I
reported in a previous email is not a specific error of the last version
of the intel compiler (12.0.0). The same error occurs with the 11.1.073
version (at least on CentOS 5.5 x86_64 arch) ..
The fix is to add the "-shared-intel" to LDFLAGS and PMEMD_LD ... ..
Below is the detailed error ..
Best
Vlad
--------error------------
make[2]: Leaving directory
`/usr/global/amber/intel-11.1.073-mvapich2-1.6rc1/AmberTools/src/arpack'
ifort -o pbsa dsvdc.o pbsa.o pb_read.o pb_write.o getcoor.o runmd.o
runmin.o force.o pb_init.o sa_driver.o np_force.o pb_force.o
pb_nlsolver.o pb_exmol.o pb_mpfrc.o pb_direct.o pb_list.o timer.o egb.o
ene.o locmem.o myopen.o rdparm.o pb_lsolver.o decomp.o rgroup.o rfree.o
debug.o ../lib/nxtsec.o
/usr/global/amber/intel-11.1.073-mvapich2-1.6rc1/lib/arpack.a
-L/usr/global/compiler/intel/11.1.073/mkl/lib/em64t -Wl,--start-group
/usr/global/compiler/intel/11.1.073/mkl/lib/em64t/libmkl_intel_lp64.a
/usr/global/compiler/intel/11.1.073/mkl/lib/em64t/libmkl_sequential.a
/usr/global/compiler/intel/11.1.073/mkl/lib/em64t/libmkl_core.a
-Wl,--end-group -lpthread -lsvml
ld: pbsa: hidden symbol `__intel_cpu_indicator_init' in
/usr/global/compiler/intel/11.1.073/lib/intel64/libirc.a(cpu_disp.o) is
referenced by DSO
ld: final link failed: Nonrepresentable section on output
make[1]: *** [pbsa] Error 1
make[1]: Leaving directory
`/usr/global/amber/intel-11.1.073-mvapich2-1.6rc1/AmberTools/src/pbsa'
make: *** [serial] Error 2
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Sat Dec 04 2010 - 03:30:03 PST
