Thanks all for the help so far, but..
A few points:
1) It is AT 1.5
2) I did apply the bugfix.
3) Under dac's warning, I reinstalled from scratch into a non "root"
directory
4) Now I have a new problem. If I unzip ambertools, patch, ./configure
-macAccelerate gnu, then make install, I get a permissions problem. Part of
the python install wants to write to my /Applications/.. directory
Considering I'm rebuilding from scratch (I completely removed my previous
installation) I don't see where the problem is coming from unless I caused
some damage with my previous sudo usage.
Appreciate any ideas...
...
/usr/bin/install -c -s ../python.exe
"/Users/sindhikara/MyPrograms/amber11/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python"
sed -e "s!%bundleid%!org.python.python!g" \
-e
"s!%version%!`DYLD_FRAMEWORK_PATH=/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6:
../python.exe \
-c 'import platform; print(platform.python_version())'`!g" \
<
"/Users/sindhikara/MyPrograms/amber11/Python.framework/Versions/2.6/Resources/Python.app/Contents/
Info.plist.in" \
>
"/Users/sindhikara/MyPrograms/amber11/Python.framework/Versions/2.6/Resources/Python.app/Contents/Info.plist"
rm
"/Users/sindhikara/MyPrograms/amber11/Python.framework/Versions/2.6/Resources/Python.app/Contents/
Info.plist.in"
DYLD_FRAMEWORK_PATH=/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6:
../python.exe ./scripts/BuildApplet.py \
--destroot "" \
--python=/Users/sindhikara/MyPrograms/amber11/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python`test
-f
"/Users/sindhikara/MyPrograms/amber11/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python-32"
&& echo "-32"` \
--output "/Applications/Python 2.6/Build Applet.app" \
./scripts/BuildApplet.py
./scripts/BuildApplet.py:37: DeprecationWarning: catching of string
exceptions is deprecated
except buildtools.BuildError, detail:
Traceback (most recent call last):
File "./scripts/BuildApplet.py", line 159, in <module>
main()
File "./scripts/BuildApplet.py", line 36, in main
buildapplet()
File "./scripts/BuildApplet.py", line 126, in buildapplet
progress=verbose, destroot=destroot)
File
"/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6/Lib/plat-mac/buildtools.py",
line 122, in process
copy_codefragment, raw, others, filename, destroot)
File
"/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6/Lib/plat-mac/buildtools.py",
line 151, in process_common
is_update, raw, others, filename, destroot)
File
"/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6/Lib/plat-mac/buildtools.py",
line 338, in process_common_macho
builder.build()
File
"/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6/Lib/plat-mac/bundlebuilder.py",
line 150, in build
shutil.rmtree(self.bundlepath)
File
"/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6/Lib/shutil.py",
line 212, in rmtree
rmtree(fullname, ignore_errors, onerror)
File
"/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6/Lib/shutil.py",
line 217, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File
"/Users/sindhikara/MyPrograms/amber11/AmberTools/src/etc/Python-2.6.6/Lib/shutil.py",
line 215, in rmtree
os.remove(fullname)
OSError: [Errno 13] Permission denied: '/Applications/Python 2.6/Build
Applet.app/Contents/Info.plist'
make[2]: *** [install_BuildApplet] Error 1
make[1]: *** [frameworkinstallapps] Error 2
make: *** [python] Error 2
2011/7/12 Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>
> Dear Dr. Daniel J. Sindhikara
>
> Hi
> I succeed in installing amber11 & AmberTools1.5 on the Mac a few days
> ago.
>
> When I installed amber11, I got the same problems.
>
> So In my case I changed the netcdf to the latest （4.1.3) .
>
>
> My method may not useful for your install.
> Because my Mac is 10.5.8.
>
>
>
> My method to install amber11
> ===============================
> patch -p0 -N < bugfix.all.A.txt (AmberTool bug fix)
> cd AmberTools/src
> cp ~/netcdf-4.1.3.tar .
> mv netcdf netcdf_old
> mkdir netcdf
> cd netcdf
> tar -xvf ../netcdf-4.1.3.tar
> mv netcdf-4.1.3/ src
> cd ../
> ./configure.tbaba -macAccelerate gnu
> make install
> cd ../../
> patch -p0 -N < ../bugfix.all_11.txt
> ./AT15_Amber11.py
> cd src
> make serial
> cd ../AmberTools/src
> cp ~/openmpi-1.4.3.tar .
> tar -xvf openmpi-1.4.3.tar
> ./configure_openmpi -np 8 gnu
> rehash
> make clean
> ./configure.tbaba -macAccelerate -mpi gnu
>
> make install
> cd ../../
> ./AT15_Amber11.py
> cd src/
> make clean
> make parallel
> ===============================
>
> If you try my method, you should the following command
>
> tar xvfj Amber11.tar.bz2
>
> If you have a question, please give me a mail.
>
> Good luck
>
> Takeshi Baba
>
>
> ----------------------------------------------------------------------------------------------------
> Takeshi Baba
>
> Graduate School of Life Science, University of Hyogo,
> 3-2-1 Koto, Kamigori, Akoh-gun, Hyogo 678-1297, Japan
> E-mail: tbaba.cheng.es.osaka-u.ac.jp
>
> ----------------------------------------------------------------------------------------------------
>
>
> On 2011/07/12, at 20:35, Daniel Sindhikara wrote:
>
> > Hello.
> > I am trying to run AMBER11 on a mac. I have been using Ambertools
> > successfully, but when I try to make serial in the $AMBERHOME/src/
> > directory
> > I get some undefined symbols when trying to make sander (from
> > command sudo
> > make serial).
> > My system is running Mac OSX10.6.8. I configured using ./configure
> > -macAccelerate gnu
> >
> > Anyone run into this issue?
> >
> >
> > Here is the start of the errors:
> > gfortran-mp-4.5 -o sander constants.o state.o memory_module.o stack.o
> > nose_hoover.o nose_hoover_vars.o nose_hoover_init.o qmmm_module.o
> > trace.o
> > lmod.o rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.o remd.o
> > findmask.o
> > relax_mat.o nmr.o multitmd.o multisander.o sander.o trajene.o cshf.o
> > nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.o mdread.o
> > locmem.o
> > runmd.o getcor.o degcnt.o decnvh.o fastwt.o parallel.o shake.o ene.o
> > mdwrit.o minrit.o set.o dynlib.o mdfil.o nmlsrc.o ew_force.o
> > ew_setup.o
> > ew_box.o ew_bspline.o ew_fft.o nonbond_list.o short_ene.o ew_recip.o
> > pcshift.o align.o csa.o rfree.o rgroup.o amopen.o debug.o
> > ew_recip_reg.o
> > ew_handle_dips.o ew_dipole_recip.o mexit.o new_time.o extra_pts.o
> > thermo_int.o matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o
> > constantph.o
> > prn_dipoles.o ips.o sglds.o iwrap2.o amoeba_valence.o
> > amoeba_multipoles.o
> > amoeba_recip.o amoeba_interface.o amoeba_direct.o amoeba_mdin.o
> > amoeba_adjust.o amoeba_self.o amoeba_vdw.o amoeba_induced.o
> > amoeba_runmd.o
> > bintraj.o spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o
> > molecule.o
> > xref.o dssp.o charmm.o qm_mm.o qm_ewald.o qm2_variable_solvent.o
> > qmmm_qmtheorymodule.o \
> > pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o cmd_matrix.o
> > lscivr_vars.o lsc_init.o lsc_xp.o force.o /usr/local/amber11/lib/
> > libsqm.a \
> > mt19937.o ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o
> > ncsu-cftree.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-
> > utils.o
> > ncsu-colvar.o ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o
> > ncsu-cv-HANDEDNESS.o ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o
> > ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o ncsu-cv-TORSION.o
> > ncsu-cv-LCOD.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-lexer.o ncsu-parser.o
> > ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o
> > ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o \
> > /usr/local/amber11/lib/libFpbsa.a /usr/local/amber11/lib/
> > arpack.a
> > -framework Accelerate ../../AmberTools/src/lib/nxtsec.o \
> > ../../AmberTools/src/lib/sys.a /usr/local/amber11/lib/
> > libnetcdf.a
> > Undefined symbols:
> > "_nf_put_varm_real_", referenced from:
> > ___netcdf_MOD_nf90_put_var_7d_fourbytereal in
> > libnetcdf.a(netcdf.o)
> > ___netcdf_MOD_nf90_put_var_6d_fourbytereal in
> > libnetcdf.a(netcdf.o)
> > ___netcdf_MOD_nf90_put_var_5d_fourbytereal in
> > libnetcdf.a(netcdf.o)
> > ___netcdf_MOD_nf90_put_var_4d_fourbytereal in
> > libnetcdf.a(netcdf.o)
> > ___netcdf_MOD_nf90_put_var_3d_fourbytereal in
> > libnetcdf.a(netcdf.o)
> > ___netcdf_MOD_nf90_put_var_2d_fourbytereal in
> > libnetcdf.a(netcdf.o)
> > ___netcdf_MOD_nf90_put_var_1d_fourbytereal in
> > libnetcdf.a(netcdf.o)
> > "_nf_delete_", referenced from:
> >
> >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sindhikara.gmail.com
> > Website: http://sites.google.com/site/dansindhikara/
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Wed Jul 13 2011 - 04:30:03 PDT
