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-- 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/amberReceived on Mon Jul 25 2011 - 19:00:03 PDT