GAMESS(US), ifort and MKL on Mac issue

Dmitry_G_ — Sun, 19 Feb 2017 18:13:34 GMT

Hello. To maximally optimize performance of quantum chemistry calculations I decided to compile GAMESS(US) using Intel toolchain and MKL on Mac, and starting lked I get the following issue:

./lked gamess 00
воскресенье, 19 февраля 2017 г. 20:31:35 (MSK)
GAMESS will be linked into the binary file gamess.00.x.
 
The name of the linker on this machine is ifort,
and the linker options are "-i8".
 
Object code list begins "gamess.o unport.o",
followed by   BLAS object code " ",
followed by LAPACK object code "dgeev.o dgesvd.o zheev.o",
followed by VECTOR object code " ",
followed by memory object code "zunix.o",
followed by the standard GAMESS object code list,
 
aldeci.o algnci.o basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.o basminix.o basn21.o basn31.o baspcn.o basg3x.o bassto.o casino.o ccaux.o ccddi.o ccqaux.o ccquad.o ccsdt.o ceeis.o cepa.o cnglob.o chgpen.o cimf.o ciminf.o cimi.o cimlib.o cimsub.o cisgrd.o comp.o cosmo.o cosprt.o cphf.o cpmchf.o cprohf.o cpuhf.o dccc.o dcgrd.o dcgues.o dcint2.o dclib.o dcmp2.o dcscf.o dctran.o ddilib.o delocl.o demrpt.o dft.o dftaux.o dftbfo.o dftbgr.o dftbhs.o dftblb.o dftbsk.o dftbtd.o dftbx.o dftdis.o dftfun.o dftgrd.o dftint.o dftxca.o dftxcb.o dftxcc.o dftxcd.o dftxce.o dftxcf.o dftxcg.o diab.o dmulti.o drc.o eaipcc.o ecp.o ecpder.o ecplib.o ecppot.o efpmodule.o efchtr.o efdrvr.o efelec.o efgrd2.o efgrda.o efgrdb.o efgrdc.o efinp.o efinta.o efintb.o efmo.o efpaul.o efpcm.o efpcov.o efpfmo.o eftei.o eigen.o elglib.o elgloc.o elgscf.o eomcc.o ewald.o excorr.o ffield.o fmo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmolib.o fmomm.o fmopbc.o fmoprp.o
frfmt.o fsodci.o g3.o globop.o gmcpt.o gradex.o guess.o grd1.o grd2a.o grd2b.o grd2c.o gugdga.o gugdgb.o gugdm.o gugdm2.o gugdrt.o gugem.o gugsrt.o gvb.o hess.o hss1a.o hss1b.o hss1c.o hss2a.o hss2b.o hss2c.o inputa.o inputb.o inputc.o int1.o int2a.o int2b.o int2c.o int2d.o int2f.o int2g.o int2r.o int2s.o iolib.o ivocas.o lagran.o local.o locatd.o loccd.o locpol.o locsvd.o lrd.o lut.o mcpgrd.o mcpinp.o mcpint.o mcpl10.o mcpl20.o mcpl30.o mcpl40.o mcpl50.o mcpl60.o mcpl70.o mcpl80.o mccas.o mcjac.o mcqdpt.o mcqdwt.o mcqud.o mcscf.o mctwo.o mdefp.o mexing.o mltfmo.o mm23.o morokm.o mnsol.o mp2.o mp2ddi.o mp2grd.o mp2gr2.o mp2ims.o mpcdat.o mpcdatpm6.o mpcgrd.o mpchbond.o mpcint.o mpcmol.o mpcmsc.o mpcpcm.o mthlib.o nameio.o nmr.o
optcix.o ordint.o ormas1.o ormpt2.o parley.o pcm.o pcmcav.o pcmcv2.o pcmder.o pcmdis.o pcmhss.o pcmief.o pcmpol.o pcmvch.o prpamm.o prpel.o prplib.o prppop.o qeigen.o qfmm.o qmfm.o qrel.o quanpo.o raman.o reorg.o rhfuhf.o ricab.o riint.o rimp2.o rmd.o rmddat.o rmdgen.o rmdwrk.o rmdrun.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.o secor.o sfdft.o sfgrad.o sobrt.o soffac.o solib.o sozeff.o statpt.o surf.o svpchg.o svpinp.o svpleb.o symhi.o symorb.o symslc.o tddft.o tddefp.o tddfun.o tddfxc.o tddgrd.o tddint.o tddnlr.o tddxca.o tddxcc.o tddxcd.o tdhf.o tdx.o tdxio.o tdxitr.o tdxni.o tdxprp.o trans.o trfdm2.o trnstn.o trudge.o umpddi.o utddft.o vibanl.o vscf.o vvos.o zapddi.o zmatrx.o
params.o
 
Choices for some optional plug-in codes are
   Tinker/SIMOMM code skipped, using dummy file qmmm.o
   Valence Bond program VB2000 object files are vb2000.o vb2gms.o
   Nuclear Electron Orbital code skipped, using dummy file neostb.o
   Natural Bond Orbital (NBO) code skipped, using dummy file nbostb.o
   MPQC code skipped, using dummy file mpqcst.o
 
   The message passing libraries searched are
/Users/dishu1/Downloads/Gamess2016R1+Libcchem/ddi/libddi.a -lpthread
 
   Other libraries, including math libraries, to be searched are
-Wl,--start-group /opt/intel/mkl/lib/libmkl_intel_ilp64.a /opt/intel/mkl/lib/libmkl_sequential.a /opt/intel/mkl/lib/libmkl_core.a -Wl,--end-group
 
Linker messages (if any) follow...
ipo: warning #11016: Warning unknown option --start-group
ipo: warning #11016: Warning unknown option --end-group
ld: unknown option: --start-group
 
Unfortunately, there was an error while linking GAMESS.
0.288u 0.796s 0:02.76 38.7%	0+0k 0+20io 4759pf+0w

Could someone please help me with ./lked script correcting to make this work? I just don't have sufficient skills to make some needed corrections by myself.

Hi Dmitry,

Ying_H_Intel — Mon, 20 Feb 2017 02:31:05 GMT

Hi Dmitry,

What compiler are you using ?

If possible, could you please try

${MKLROOT}/lib/libmkl_intel_ilp64.a ${MKLROOT}/lib/libmkl_sequential.a ${MKLROOT}/lib/libmkl_core.a -lpthread -lm -ldl

without the --start-group and --end-group. to see if any change.

Here are two on-line article for your reference:

Building the GAMESS with Intel® Compilers, Intel® MKL and Intel® MPI on Linux (you can ignore MPI part if you don't need)

https://software.intel.com/en-us/articles/building-gamess-with-intel-compilers-intel-mkl-and-intel-mpi-on-linux/

and the similar issue:

https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/621814

https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/

Best Regards,
Ying

topic Hi Dmitry, in Intel® oneAPI Math Kernel Library

GAMESS(US), ifort and MKL on Mac issue

Hi Dmitry,