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
----------------------------------------------------------------------------------------------------
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Received on Wed Jul 13 2011 - 04:30:03 PDT
