Jason,
Thanks, yes that did fix *that* problem (despite it not making sense).
Takeshi, you gave instructions on each step but have a modified version of
configure and a separate netcdf. What is different about the configure and
netcdf? About 'linking gcc45', did you only link gcc45 or also gfortran and
g++?
--Dan
On Tue, Jul 26, 2011 at 10:32 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Try configuring with -nopython. It should still be able to run the Python
> programs there.
>
> However, I haven't had issues building Python on my Mac. It should use the
> Xcode GCC by default. I haven't followed the thread long enough, but I can
> look into it more in a week or so.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Jul 25, 2011, at 3:10 AM, Daniel Sindhikara <sindhikara.gmail.com>
> wrote:
>
> > 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
>
> _______________________________________________
> 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 Tue Jul 26 2011 - 03:00:04 PDT
