CCL: GAMESS Linking Error (Atlas)
- From: "Salter-Duke, Brian James -"
<brian.james.duke%gmail.com>
- Subject: CCL: GAMESS Linking Error (Atlas)
- Date: Wed, 15 Jan 2020 07:26:32 +1100
Sent to CCL by: "Salter-Duke, Brian James -"
[brian.james.duke!^!gmail.com]
In these lines:-
> prec.o params.o mpqcst.o -L/usr/lib64/atlas -lf77blas -latlas -
> L/usr/lib64/atlas -lf77blas -latlas /scratch/user330/gamess/ddi/libddi.a -
you appear to be repeating -L/usr/lib64/atlas -lf77blas -latlas. Are blas and
atlas in -L/usr/lib64/atlas? Or do your need something like:-
-L/usr/lib64/blas -lf77blas -L/usr/lib64/atlas -latlas ?
Brian.
On Tue, Jan 14, 2020 at 08:09:21AM -0500, Min Jae Kim kjh950429 _ gmail.com
wrote:
>
> Sent to CCL by: "Min Jae Kim" [kjh950429%%gmail.com]
> Dear all,
>
> I am currently trying to set up GAMESS on a super computer, and was
> encountering errors trying to link an executable form of GAMESS. I am
> currently working in a linux64 machine. My FORTRAN Compiler setup is
gfortran
> (ver. 4.8) with openmpi and using a atlas-so library.
>
> I have located the atlas libraries on the machine I'm working with, but
they
> seemed to be divided into two: libsatlas.so.3.10, libtatlas.so.3.10. There
> were also pre-made links to these libraries in the same directory--
> libsatlas.so.3 and libtatlas.so.3 respectively.
>
> When I run the lked command, I get the following lked.log file:
>
> GAMESS will be linked into the binary file gamess.01.x.
>
> The name of the linker on this machine is gfortran,
> and the linker options are " ".
>
> 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 ... (I deleted rest of the list in this email to save
> length)
>
> Choices for some optional plug-in codes are
> Tinker/SIMOMM code skipped, using dummy file qmmm.o
> Both VB programs skipped, using dummy file vbdum.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
> /scratch/user330/gamess/ddi/libddi.a -L/usr/include/openmpi-x86_64/lib
-lmpi
> -lpthread
>
> Other libraries, including math libraries, to be searched are
> -L/usr/lib64/atlas -lf77blas -latlas
>
> Linker messages (if any) follow...
> dgeev.o dgesvd.o zheev.o
> gfortran -L/scratch/user330/gamess/libcchem/boost/lib -o
> /scratch/user330/gamess/gamess.01.x -I/scratch/user330/gamess/object
gamess.o
> unport.o dgeev.o dgesvd.o zheev.o zunix.o 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 efmograd.o
> efmograd_es.o efmograd_exrep.o efmograd_disp.o efmograd_pol.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 fmoafo.o fmocp.o fmoesd.o fmogrd.o fmoh1a.o
> fmoh2a.o fmoh2b.o fmoh2c.o fmohss.o fmoint.o fmoio.o fmoio_read.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 modmcpdft.o mcpdft.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 modmnfun.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 nebpath.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 rimp2omp.o rimp2grd.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 hrmrst.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_m05.o
> tddxcd_m06.o tddxcd_m08.o tddxcd_pkzb.o tddxcd_revtpss.o tddxcd_tpss.o
> tddxcd_vs98.o tddxce.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 utdgrd.o vibanl.o vscf.o
vvos.o
> zapddi.o zmatrx.o mod_nosp_basis.o mod_grid_storage.o mod_dft_partfunc.o
> mod_dft_molgrid.o mod_dft_fuzzycell.o mod_dft_gridint.o ccsd3aacgreorder.o
> ccsd3aacgsum.o ccsd3aacgt1A00.o ccsd3aacgt1A01.o ccsd3aacgt1A10.o
> ccsd3aacgt1A11.o ccsd3aacgt1A.o ccsd3aacgt1B00.o ccsd3aacgt1B01.o
> ccsd3aacgt1B10.o ccsd3aacgt1B11.o ccsd3aacgt1B.o ccsd3aacgt2A0000.o
> ccsd3aacgt2A0010.o ccsd3aacgt2A0011.o ccsd3aacgt2A1000.o ccsd3aacgt2A1010.o
> ccsd3aacgt2A1011.o ccsd3aacgt2A1100.o ccsd3aacgt2A1110.o ccsd3aacgt2A1111.o
> ccsd3aacgt2A1.o ccsd3aacgt2A.o ccsd3aacgt2B0000.o ccsd3aacgt2B0001.o
> ccsd3aacgt2B0010.o ccsd3aacgt2B0011.o ccsd3aacgt2B0100.o ccsd3aacgt2B0101.o
> ccsd3aacgt2B0110.o ccsd3aacgt2B0111.o ccsd3aacgt2B1000.o ccsd3aacgt2B1001.o
> ccsd3aacgt2B1010.o ccsd3aacgt2B1011.o ccsd3aacgt2B1100.o ccsd3aacgt2B1101.o
> ccsd3aacgt2B1110.o ccsd3aacgt2B1111.o ccsd3aacgt2B1.o ccsd3aacgt2B.o
> ccsd3aacgt2C0000.o ccsd3aacgt2C0010.o ccsd3aacgt2C0011.o ccsd3aacgt2C1000.o
> ccsd3aacgt2C1010.o ccsd3aacgt2C1011.o ccsd3aacgt2C1100.o ccsd3aacgt2C1110.o
> ccsd3aacgt2C1111.o ccsd3aacgt2C1.o ccsd3aacgt2C.o ccsd3aacgt3A100100.o
> ccsd3aacgt3A100110.o ccsd3aacgt3A100111.o ccsd3aacgt3A110100.o
> ccsd3aacgt3A110110.o ccsd3aacgt3A110111.o ccsd3aacgt3A111100.o
> ccsd3aacgt3A111110.o ccsd3aacgt3A111111.o ccsd3aacgt3AB.o
> ccsd3aacgt3B001001.o ccsd3aacgt3B001100.o ccsd3aacgt3B001101.o
> ccsd3aacgt3B001110.o ccsd3aacgt3B001111.o ccsd3aacgt3B100001.o
> ccsd3aacgt3B100100.o ccsd3aacgt3B100101.o ccsd3aacgt3B100110.o
> ccsd3aacgt3B100111.o ccsd3aacgt3B101001.o ccsd3aacgt3B101100.o
> ccsd3aacgt3B101101.o ccsd3aacgt3B101110.o ccsd3aacgt3B101111.o
> ccsd3aacgt3B110001.o ccsd3aacgt3B110100.o ccsd3aacgt3B110101.o
> ccsd3aacgt3B110110.o ccsd3aacgt3B110111.o ccsd3aacgt3B111001.o
> ccsd3aacgt3B111100.o ccsd3aacgt3B111101.o ccsd3aacgt3B111110.o
> ccsd3aacgt3B111111.o ccsd3aacgt3BC.o ccsd3aacgt3C010010.o
> ccsd3aacgt3C010011.o ccsd3aacgt3C010100.o ccsd3aacgt3C010110.o
> ccsd3aacgt3C010111.o ccsd3aacgt3C011010.o ccsd3aacgt3C011011.o
> ccsd3aacgt3C011100.o ccsd3aacgt3C011110.o ccsd3aacgt3C011111.o
> ccsd3aacgt3C100010.o ccsd3aacgt3C100011.o ccsd3aacgt3C100100.o
> ccsd3aacgt3C100110.o ccsd3aacgt3C100111.o ccsd3aacgt3C110010.o
> ccsd3aacgt3C110011.o ccsd3aacgt3C110100.o ccsd3aacgt3C110110.o
> ccsd3aacgt3C110111.o ccsd3aacgt3C111010.o ccsd3aacgt3C111011.o
> ccsd3aacgt3C111100.o ccsd3aacgt3C111110.o ccsd3aacgt3C111111.o
> ccsd3aacgt3CD.o ccsd3aacgt3D100100.o ccsd3aacgt3D100110.o
> ccsd3aacgt3D100111.o ccsd3aacgt3D110100.o ccsd3aacgt3D110110.o
> ccsd3aacgt3D110111.o ccsd3aacgt3D111100.o ccsd3aacgt3D111110.o
> ccsd3aacgt3D111111.o ccsd3amain.o qmmm.o vbdum.o neostb.o nbostb.o cchdmy.o
> prec.o params.o mpqcst.o -L/usr/lib64/atlas -lf77blas -latlas -
> L/usr/lib64/atlas -lf77blas -latlas /scratch/user330/gamess/ddi/libddi.a -
> L/usr/include/openmpi-x86_64/lib -lmpi -lpthread
> /usr/bin/ld: cannot find -lf77blas
> /usr/bin/ld: cannot find -latlas
> /usr/bin/ld: cannot find -lf77blas
> /usr/bin/ld: cannot find -latlas
> /usr/bin/ld: cannot find -lmpi
> collect2: error: ld returned 1 exit status
> set rc=1
> unset echo
>
> Unfortunately, there was an error while linking GAMESS.
> 0.379u 0.553s 0:01.19 77.3% 0+0k 0+40io 0pf+0w
>
> I would really appreciate any advice or help on this issue. Thank you.>
--
Brian Salter-Duke (Brian Duke) Brian.Salter-Duke^monash.edu
Adjunct Associate Professor
Monash Institute of Pharmaceutical Sciences
Monash University Parkville Campus, VIC 3052, Australia