> On Nov 20, 2014, at 9:31 PM, Biao Ma <jackyma1981.gmail.com> wrote:
>
> Hi, amber users.
>
> When I install the amber12 on my Ubuntu pc, I got the error messge when I
> do 'make install'.
> what I did is :
>
> #####################
> # First time I did
> #####################
>
> 1.
>
> sudo apt-get update
> 2.
>
> sudo apt-get install csh flex patch gfortran g++ make xorg-dev libbz2-dev
> 3.
>
> sudo apt-get install python-tk python-dev python-matplotlib python-numpy
> python-scipy
> 4.
>
> sudo apt-get install openmpi-bin libopenmpi-dev
> 5.
>
> cd $AMBERHOME && make clean (the source files is copyed from another
> Linux PC, which was successed installed amber by ./configure -mpi -rism
> intel, make install)
> 6.
>
> ./configure gnu
> 7. make install (Error is out)
>
>
>
> the last part of stdout message after 'make install':
>
> cd ../lib && make nxtsec.o random.o
> make[3]: Entering directory `/home/mabiao/bin/amber12/AmberTools/src/lib'
> make[3]: `nxtsec.o' is up to date.
> make[3]: `random.o' is up to date.
> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/lib'
> cd ../lapack && make install
> make[3]: Entering directory `/home/mabiao/bin/amber12/AmberTools/src/lapack'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/lapack'
> cd ../blas && make install
> make[3]: Entering directory `/home/mabiao/bin/amber12/AmberTools/src/blas'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/blas'
> cd ../arpack && make install
> make[3]: Entering directory `/home/mabiao/bin/amber12/AmberTools/src/arpack'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/arpack'
> gfortran -DFFTW -DBINTRAJ -ffree-form
> -I/home/mabiao/bin/amber12/include -I/home/mabiao/bin/amber12/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/home/mabiao/bin/amber12/lib -larpack -llapack -lblas
> /usr/bin/ld: skipping incompatible /home/mabiao/bin/amber12/lib/libfftw3.a
> when searching for -lfftw3
> /usr/bin/ld: cannot find -lfftw3
> collect2: error: ld returned 1 exit status
> make[2]: *** [pbsa] Error 1
> make[2]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/pbsa'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src'
> make: *** [install] Error 2
>
> when I check the folder ~/amber12/lib/ I found some older files was created
> at 2013,
> -rw-r--r-- 1 mabiao mabiao 3.0M Nov 28 2013 libfftw3.a
> -rw-r--r-- 1 mabiao mabiao 80K Nov 28 2013 libxblas-amb.a
> -rw-r--r-- 1 mabiao mabiao 1.2M Nov 28 2013 libnab.a
> -rw-r--r-- 1 mabiao mabiao 1.6M Nov 28 2013 libnetcdf.a
> -rwxr-xr-x 1 mabiao mabiao 898 Nov 20 15:02 libDiagnostics.la
> -rw-r--r-- 1 mabiao mabiao 5.8K Nov 20 15:02 libDiagnostics.a
> -rwxr-xr-x 1 mabiao mabiao 886 Nov 20 15:02 libtinyxml.la
> -rw-r--r-- 1 mabiao mabiao 120K Nov 20 15:02 libtinyxml.a
>
> why the old file not removed when 'make clean’?
Because they shouldn’t be. This is a task for “make uninstall”, not “make clean” (if “make clean” got rid of these files, then “make clean” would effectively uninstall Amber each time!)
>
> #####################
> # second time I did
> #####################
>
> I try to delete all the files in $AMBERHOME/lib/, and then do
> make clean
> ./configure gnu
> make install
>
> this time I got the another error message
>
> gcc: error: /home/mabiao/bin/amber12/lib/libnetcdf.a: No such file or
> directory
> make[2]: *** [rdparm] Error 1
> make[2]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src/ptraj'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/home/mabiao/bin/amber12/AmberTools/src'
> make: *** [install] Error 2
>
> I check the $AMBERHOME/lib/ folder and found there no libnetcdf.a ,
>
> The files in $AMBERHOME/lib/ folder how to be generated ?
> Who can give me some advice ?
Upgrade to AmberTools 14, or start from a fresh copy of AmberTools 12 + Amber 12.
If that’s not plausible, run the command “make clean uninstall” and try to start from there.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 20 2014 - 19:30:03 PST
