Hi,
could you install the last Intel Fortran and C Composer XE for Linux.
Amber12 and AmberTools13 compile in a clean way with them. At least in
Centos6.2
Best Wishes,
Hector.
> 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
> make[2]: *** [pbsa] Error 1
> make[2]: Leaving directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src/pbsa'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory
> `/home/srg/nadun/ambertools/amber12/AmberTools/src'
> make: *** [install] Error 2
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4423789 ext. 157
--------------------------------------
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AMBER mailing list
AMBER.ambermd.org
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Received on Sat May 04 2013 - 17:30:04 PDT
