Takeshi,
It took a while to reply, sorry about that. I understand that it worked
for you but I'm still getting the same permissions error when I try to
install. I am using gcc 4.5 from macports, but I still don't see how that is
related to the python permissions error. In your workflow I don't see
anything about python. Are you saying I should replace the python 2.6.6
directory with 2.6?
-Dan
2011/7/14 Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>
> Now I tried to install amber11 on the Mac OS10.6.8
>
>
> Before installing amber11, I got gcc45 from Macports and make a link
>
> >>>> 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
> >>>>
> >>>>
> >>>> ===============================
> >>
>
>
> I succeeded in installing amber11 (serial)
>
> *My machine is iMac .
>
> If you have a time you should start from the following command.
>
> tar xvfj AmberToos-1.5.tar.bz2
>
>
> Good luck
>
> Takeshi Baba
>
> On 2011/07/14, at 11:44, Daniel Sindhikara wrote:
>
> > 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/
> > --
> > _______________________________________________
> > 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/
--
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 25 2011 - 00:30:02 PDT
