Hi, Jason
Thankｓ for your answer.
I completed install from a fresh copy of AmberTools 12 + Amber 12.
jacky
***************************************************************************
馬 彪 （マ ヒョウ）
501-1193 岐阜柳戸１－１
岐阜大学 大学院連合創薬医療情報研究科
医療情報学専攻 博士課程
TEL:058-230-6143(内線8261), FAX:058-230-6144
E-mail:
s3502003.edu.gifu-u.ac.jp, jackyma1981.gmail.com
URL: http://www1.gifu-u.ac.jp/~ceid/
***************************************************************************
On Fri, Nov 21, 2014 at 12:06 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> > 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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>
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Received on Mon Nov 24 2014 - 18:30:02 PST
