Dear Daniel J. Sindhikara
I think you don't have to change the Python version.
When you start " tar xvfj AmberTools", Python 2.6.6 is installed in
the Directory: ($AMBERHOME/AmberTools/src/etc)
Next you make configure " ./configure -macAcceletrate gnu" , and you
will get the config.h.
Please check your config.log in the Python-2.6.6 directory.
My config.log " is ./configure CC=usr/bin/gcc-4.2 --enable-framework=
$AMBERHOME --prefix=$AMBERHOME --enable-ipv6"
First of all, please check you config.log. "gcc-4.2" is very
important. gcc-4.5 doesn't work in the Python2.6.6.
If you have a problem, please send me a mail.
Good Luck
Takeshi Baba
On 2011/07/25, at 16:10, Daniel Sindhikara 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
>
----------------------------------------------------------------------------------------------------
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 Mon Jul 25 2011 - 01:30:02 PDT
