Hi,
This looks like an MKL issue. Can you compile after configuring with
MKL_HOME unset?
-Dan
On Wed, Jun 5, 2013 at 12:23 PM, Jonathan Gough
<jonathan.d.gough.gmail.com> wrote:
> I'm really confused... I've compiled amber several times over, and I
> haven't run into this error until now. can anyone provide any insight?
>
> CentOS6
> ./configure gnu
>
> make install
>
> errors are:
> make[3]: Entering directory `/share/apps/amber12/AmberTools/src/lib'
> make[3]: `nxtsec.o' is up to date.
> make[3]: `random.o' is up to date.
> make[3]: Leaving directory `/share/apps/amber12/AmberTools/src/lib'
> cd ../lapack && make skip
> make[3]: Entering directory `/share/apps/amber12/AmberTools/src/lapack'
> skipping compilation of LAPACK
> make[3]: Leaving directory `/share/apps/amber12/AmberTools/src/lapack'
> cd ../blas && make skip
> make[3]: Entering directory `/share/apps/amber12/AmberTools/src/blas'
> skipping compilation of BLAS
> make[3]: Leaving directory `/share/apps/amber12/AmberTools/src/blas'
> cd ../arpack && make install
> make[3]: Entering directory `/share/apps/amber12/AmberTools/src/arpack'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/share/apps/amber12/AmberTools/src/arpack'
> gfortran -DFFTW -DMKL -DBINTRAJ -ffree-form
> -I/share/apps/amber12/include -I/share/apps/amber12/include
> -I/opt/intel/composer_xe_2013.3.163/mkl/include -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_fddrv.o pb_iimdrv.o pb_nlsolver.o
> pb_exmol.o pb_mpfrc.o pb_direct.o pb_list.o timer.o pb_fftsolv.o pb_fft.o
> egb.o ene.o locmem.o myopen.o rdparm.o pb_lsolver.o decomp.o rgroup.o
> rfree.o debug.o coed20.o indexg.o irre32.o phidev.o project.o qld.o
> coed6.o irre31.o miniop.o iimod.o prodis.o qint.o wint.o transf.o
> curv.o GrToPr.o jumps.o problem.o IIM.o regular.o gmres.o daxpy.o ddot.o
> dheqr.o dpigmr.o dscal.o dslui2.o dxlcal.o dchkw.o dgmres.o dnrm2.o
> drlcal.o dsilus.o dslui.o isdgmr.o dcopy.o dhels.o dorth.o ds2y.o
> dslugm.o dsmv.o qs2i1d.o d1mach.o fdump.o i1mach.o j4save.o
> xercnt.o xerhlt.o xermsg.o xerprn.o xersve.o xgetua.o bicg.o dbcg.o
> dslui4.o dsluti.o dsmtv.o dslubc.o isdbcg.o pb_chkfrc.o svdcmp.o svbksb.o
> pythag.o pb_augdrv.o gmresX.o interpX.o matvec3.o gen_dx_file.o aug_iccg.o
> membrane.o fftw3.o \
> ../lib/nxtsec.o ../lib/random.o -lfftw3 \
> -L/share/apps/amber12/lib -larpack -Wl,--start-group
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_lp64.a
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_sequential.a
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a
> -Wl,--end-group -lpthread
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a(ueaa_prv_load_backend_lib.o):
> In function `ueaa_prv_load_backend_libs':
> ueaa_prv_load_backend_lib.c:(.text+0x263): undefined reference to `dlopen'
> ueaa_prv_load_backend_lib.c:(.text+0x28c): undefined reference to `dlsym'
> ueaa_prv_load_backend_lib.c:(.text+0x2ae): undefined reference to `dlsym'
> ueaa_prv_load_backend_lib.c:(.text+0x2d0): undefined reference to `dlsym'
> ueaa_prv_load_backend_lib.c:(.text+0x2f2): undefined reference to `dlsym'
> ueaa_prv_load_backend_lib.c:(.text+0x314): undefined reference to `dlsym'
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a(ueaa_prv_load_backend_lib.o):ueaa_prv_load_backend_lib.c:(.text+0x336):
> more undefined references to `dlsym' follow
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a(mkl_libc_is_static.o):
> In function `mkl_serv_libc_is_static':
> ../../../../serv/kernel/mkl_libc_is_static.c:(.text+0x10): undefined
> reference to `dladdr'
> /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a(mkl_aa_fw_load_orsl_light_lib.o):
> In function `mkl_aa_fw_load_orsl_light_lib':
> ../../../../serv/offload/framework/core/mkl_aa_fw_load_orsl_light_lib.c:(.text+0xd3):
> undefined reference to `dlopen'
> ../../../../serv/offload/framework/core/mkl_aa_fw_load_orsl_light_lib.c:(.text+0xfc):
> undefined reference to `dlsym'
> ../../../../serv/offload/framework/core/mkl_aa_fw_load_orsl_light_lib.c:(.text+0x11a):
> undefined reference to `dlsym'
> ../../../../serv/offload/framework/core/mkl_aa_fw_load_orsl_light_lib.c:(.text+0x138):
> undefined reference to `dlsym'
> ../../../../serv/offload/framework/core/mkl_aa_fw_load_orsl_light_lib.c:(.text+0x156):
> undefined reference to `dlsym'
> collect2: ld returned 1 exit status
> make[2]: *** [pbsa] Error 1
> make[2]: Leaving directory `/share/apps/amber12/AmberTools/src/pbsa'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/share/apps/amber12/AmberTools/src'
> make: *** [install] Error 2
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 05 2013 - 12:00:02 PDT
