Error with MKL and GAMESS

npetelski — Wed, 23 Mar 2016 05:32:17 GMT

Hello guys!

I've been trying to install GAMESS software and I'm mired on a particular step.

I'm using the official guide provided with the software, and when I get to this step:

./lked gamess 01 >& lked.log &

This should produce the executable image 'gamess.01.x' (link), but instead I received this message:

mié mar 16 17:30:54 ART 2016
GAMESS will be linked into the binary file gamess.00.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 basccn.o basecp.o basext.o basg3l.o bashuz.o bashz2.o baskar.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 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 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 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 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 hss2a.o hss2b.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 loccd.o locpol.o locsvd.o lrd.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 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 rhfuhf.o ricab.o riint.o rimp2.o rmd.o rmddat.o rmdgen.o rmdwrk.o roeom.o rohfcc.o rxncrd.o ryspol.o scflib.o scfmi.o scrf.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

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
/usr/local/gamess/ddi/libddi.a -lpthread

   Other libraries, including math libraries, to be searched are
-Wl,--start-group /opt/intel/mkl/lib/intel64/libmkl_gf_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_sequential.a /opt/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group

Linker messages (if any) follow...
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o): En la función `mkl_serv_set_memory_limit':
mkl_memory.c:(.text+0x49c): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x4b2): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x4c8): referencia a `dlsym' sin definir
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o): En la función `mkl_serv_allocate':
mkl_memory.c:(.text+0x1251): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x1267): referencia a `dlsym' sin definir
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o):mkl_memory.c:(.text+0x127d): más referencias a `dlsym' sin definir a continuación
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o): En la función `mm_cleanup_thread_cbk':
mkl_memory.c:(.text+0x66df): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x66ff): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x6715): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x672b): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x67bf): referencia a `dlerror' sin definir
mkl_memory.c:(.text+0x6812): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x68c6): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x68dc): referencia a `dlerror' sin definir
mkl_memory.c:(.text+0x69a3): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x69ab): referencia a `dlerror' sin definir
mkl_memory.c:(.text+0x69bb): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x69de): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x69e6): referencia a `dlerror' sin definir
mkl_memory.c:(.text+0x69f9): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x6a14): referencia a `dlerror' sin definir
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o): En la función `MKL_Load_Lib':
mkl_memory.c:(.text+0x6c3e): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x6c48): referencia a `dlerror' sin definir
mkl_memory.c:(.text+0x6c9b): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x6d54): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x6d6e): referencia a `dlerror' sin definir
mkl_memory.c:(.text+0x6e3b): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x6e43): referencia a `dlerror' sin definir
mkl_memory.c:(.text+0x6e53): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x6e76): referencia a `dlopen' sin definir
mkl_memory.c:(.text+0x6e7e): referencia a `dlerror' sin definir
mkl_memory.c:(.text+0x6e8e): referencia a `dlsym' sin definir
mkl_memory.c:(.text+0x6ea9): referencia a `dlerror' sin definir
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_memory_patched.o): En la función `_Init_MKL_Loader':
mkl_memory.c:(.text+0x6ee0): referencia a `dladdr' sin definir
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_aa_fw_load_orsl_lite_lib_HOST.o): En la función `mkl_aa_fw_load_orsl_lite_lib':
mkl_aa_fw_load_orsl_lite_lib.c:(.text+0xb9): referencia a `dlopen' sin definir
mkl_aa_fw_load_orsl_lite_lib.c:(.text+0xd4): referencia a `dlsym' sin definir
mkl_aa_fw_load_orsl_lite_lib.c:(.text+0xf2): referencia a `dlsym' sin definir
mkl_aa_fw_load_orsl_lite_lib.c:(.text+0x110): referencia a `dlsym' sin definir
mkl_aa_fw_load_orsl_lite_lib.c:(.text+0x12e): referencia a `dlsym' sin definir
/opt/intel/mkl/lib/intel64/libmkl_core.a(load_library_HOST.o): En la función `mkl_ueaa_prv_load_backend_lib':
load_library.c:(.text+0x1cd): referencia a `dlopen' sin definir
load_library.c:(.text+0x1ef): referencia a `dlvsym' sin definir
load_library.c:(.text+0x218): referencia a `dlvsym' sin definir
load_library.c:(.text+0x241): referencia a `dlvsym' sin definir
load_library.c:(.text+0x26a): referencia a `dlvsym' sin definir
load_library.c:(.text+0x293): referencia a `dlvsym' sin definir
/opt/intel/mkl/lib/intel64/libmkl_core.a(load_library_HOST.o):load_library.c:(.text+0x2bc): más referencias a `dlvsym' sin definir a continuación
/opt/intel/mkl/lib/intel64/libmkl_core.a(mkl_libc_is_static.o): En la función `mkl_serv_libc_is_static':
mkl_libc_is_static.c:(.text+0x10): referencia a `dladdr' sin definir
collect2: error: ld returned 1 exit status

Unfortunately, there was an error while linking GAMESS.
0.4u 0.1s 0:00.51 98.0% 0+0k 0+76616io 0pf+0w

Does anyone have a clue about this error?
Really I don't know if this error is particular of GAMESS or it could be an error of MKL.

PD: Sorry for the bad English.

Symbol dlopen is provided by

Dmitry_B_Intel — Fri, 08 Apr 2016 11:15:02 GMT

Symbol dlopen is provided by libdl. You should add -ldl on the link line (see also MKL link advisor).

Thanks
Dima

Quote:Dmitry Baksheev (Intel)

Aleksandar_O_ — Wed, 26 Apr 2017 14:27:30 GMT

Dmitry Baksheev (Intel) wrote:

Symbol dlopen is provided by libdl. You should add -ldl on the link line (see also MKL link advisor).

Thanks
Dima

I have the same problem but I have no clue what I should do.

Add -ldl to the linker flags.

mecej4 — Wed, 26 Apr 2017 15:15:20 GMT

Add -ldl to the linker flags.

Quote:mecej4 wrote:

Aleksandar_O_ — Fri, 28 Apr 2017 09:17:49 GMT

mecej4 wrote:

Add -ldl to the linker flags.

I understand that, but I have no idea where I should add -ldl. May be I should add in the lked file?

I had the same problem and

dion__francois — Thu, 21 Dec 2017 19:35:23 GMT

I had the same problem and adding -ldl to the linker flags was the correct workaround.

Edit the file lked and change to line :

set EXTRA_LINK_FLAGS=''

set EXTRA_LINK_FLAGS='-ldl'