I'm not sure what you mean here. Python 2.6.6 is included in the ambertools
tarball.
Are you saying I should replace it with a different version?
2011/7/13 Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>
> Hi
> you check the python in your configure.
> I think you should use gcc4.2 to install Python2.6 in the amber11.
>
> when you make clean in the ambertools, Python2.6.6 is removed.
> So you try to start to unzip ambertools again.
>
> If you get something wrong or same problems,
> please give me a mail
>
> good luck.
>
> Takeshi Baba
> On 2011/07/13, at 20:01, Daniel Sindhikara wrote:
>
> > 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/
> > --
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ----------------------------------------------------------------------------------------------------
> 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
>
> ----------------------------------------------------------------------------------------------------
>
>
>
>
>
>
> _______________________________________________
> 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 - 20:00:03 PDT
