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'?
#####################
# 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 ?
Thanks a lot.
Jacky
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Received on Thu Nov 20 2014 - 19:00:02 PST
