On Sat, May 4, 2013 at 4:21 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>wrote:
> HI
>
> I found the following error while compiling the ambertools13. I started
> with AmberTools13.tar.bz2 as instructed in AmberTools13.pdf user manual. I
> tried both intel and gnu compilers, but both failed. I followed the steps,
> however skipped the step 3 as I already have the compilers.
>
> Thank you
>
> Chinthaka
>
> make[3]: Entering directory `/home/srg/nadun/ambertools/
> amber12/AmberTools/src/lib'
> make[3]: Warning: File `nxtsec.o' has modification time 1.9e+02 s in the
> future
> make[3]: `nxtsec.o' is up to date.
> make[3]: `random.o' is up to date.
> make[3]: warning: Clock skew detected. Your build may be incomplete.
> make[3]: Leaving directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src/lib'
> cd ../lapack && make skip
> make[3]: Entering directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src/lapack'
> skipping compilation of LAPACK
> make[3]: Leaving directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src/lapack'
> cd ../blas && make skip
> make[3]: Entering directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src/blas'
> skipping compilation of BLAS
> make[3]: Leaving directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src/blas'
> cd ../arpack && make install
> make[3]: Entering directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src/arpack'
> make[3]: Warning: File `/home/srg/nadun/ambertools/amber12/lib/libarpack.a'
> has modification time 1.9e+02 s in the future
> make[3]: Nothing to be done for `install'.
> make[3]: warning: Clock skew detected. Your build may be incomplete.
> make[3]: Leaving directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src/arpack'
> gfortran -DMKL -DBINTRAJ -ffree-form
> -I/home/srg/nadun/ambertools/amber12/include
> -I/home/srg/nadun/ambertools/amber12/include
> -I/opt/intel/cmkl/9.1.021/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 \
> -L/home/srg/nadun/ambertools/amber12/lib -larpack
> -Wl,--start-group /opt/intel/cmkl/9.1.021/lib/em64t/libmkl_intel_lp64.a
> /opt/intel/cmkl/9.1.021/lib/em64t/libmkl_sequential.a
> /opt/intel/cmkl/9.1.021/lib/em64t/libmkl_core.a -Wl,--end-group
> -lpthread
> gfortran: /opt/intel/cmkl/9.1.021/lib/em64t/libmkl_intel_lp64.a: No such
> file or directory
> gfortran: /opt/intel/cmkl/9.1.021/lib/em64t/libmkl_sequential.a: No such
> file or directory
> gfortran: /opt/intel/cmkl/9.1.021/lib/em64t/libmkl_core.a: No such file or
> directory
>
Stop trying to use the Intel MKL libraries. Your intel compiler version is
too old and it appears that the library files are not what we expect them
to be in the configure script.
Make sure that the MKL_HOME environment variable is _not_ set, then run
configure again. You can do this in bash by:
unset MKL_HOME
You can do this in csh or tcsh by the command:
unsetenv MKL_HOME
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat May 04 2013 - 17:30:02 PDT
