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
----------------------------------------------------------------------------------------------------
_______________________________________________
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AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 13 2011 - 22:30:02 PDT
