Cholmod is optional for isd, and also only deprecated stuff uses it. I'd force the config to compile without cholmod if I knew how.

On 20 mai 2012, at 07:22, Seung Joong Kim sjkim@salilab.org wrote:

> There is only one libchomod in my mac > > /opt/local/lib/libcholmod.a > > Here is the result of "otool -L". Not sure how much helpful this information is.. By the way, I need to enable the "ISD" module, since it is required by the "SAXS_merge" module... If there is no easy solution, I will stick to use the linux machine. Thanks a lot! > > [sjkim@MAC /opt/local/lib]$ otool -L libcholmod.a > Archive : libcholmod.a > libcholmod.a(cholmod_aat.o): > libcholmod.a(cholmod_add.o): > libcholmod.a(cholmod_band.o): > libcholmod.a(cholmod_change_factor.o): > libcholmod.a(cholmod_common.o): > libcholmod.a(cholmod_complex.o): > libcholmod.a(cholmod_copy.o): > libcholmod.a(cholmod_dense.o): > libcholmod.a(cholmod_error.o): > libcholmod.a(cholmod_factor.o): > libcholmod.a(cholmod_memory.o): > libcholmod.a(cholmod_sparse.o): > libcholmod.a(cholmod_transpose.o): > libcholmod.a(cholmod_triplet.o): > libcholmod.a(cholmod_check.o): > libcholmod.a(cholmod_read.o): > libcholmod.a(cholmod_write.o): > libcholmod.a(cholmod_amd.o): > libcholmod.a(cholmod_analyze.o): > libcholmod.a(cholmod_colamd.o): > libcholmod.a(cholmod_etree.o): > libcholmod.a(cholmod_factorize.o): > libcholmod.a(cholmod_postorder.o): > libcholmod.a(cholmod_rcond.o): > libcholmod.a(cholmod_resymbol.o): > libcholmod.a(cholmod_rowcolcounts.o): > libcholmod.a(cholmod_rowfac.o): > libcholmod.a(cholmod_solve.o): > libcholmod.a(cholmod_spsolve.o): > libcholmod.a(cholmod_drop.o): > libcholmod.a(cholmod_horzcat.o): > libcholmod.a(cholmod_norm.o): > libcholmod.a(cholmod_scale.o): > libcholmod.a(cholmod_sdmult.o): > libcholmod.a(cholmod_ssmult.o): > libcholmod.a(cholmod_submatrix.o): > libcholmod.a(cholmod_vertcat.o): > libcholmod.a(cholmod_symmetry.o): > libcholmod.a(cholmod_rowadd.o): > libcholmod.a(cholmod_rowdel.o): > libcholmod.a(cholmod_updown.o): > libcholmod.a(cholmod_super_numeric.o): > libcholmod.a(cholmod_super_solve.o): > libcholmod.a(cholmod_super_symbolic.o): > libcholmod.a(cholmod_ccolamd.o): > libcholmod.a(cholmod_csymamd.o): > libcholmod.a(cholmod_metis.o): > libcholmod.a(cholmod_nesdis.o): > libcholmod.a(cholmod_camd.o): > libcholmod.a(cholmod_l_aat.o): > libcholmod.a(cholmod_l_add.o): > libcholmod.a(cholmod_l_band.o): > libcholmod.a(cholmod_l_change_factor.o): > libcholmod.a(cholmod_l_common.o): > libcholmod.a(cholmod_l_complex.o): > libcholmod.a(cholmod_l_copy.o): > libcholmod.a(cholmod_l_dense.o): > libcholmod.a(cholmod_l_error.o): > libcholmod.a(cholmod_l_factor.o): > libcholmod.a(cholmod_l_memory.o): > libcholmod.a(cholmod_l_sparse.o): > libcholmod.a(cholmod_l_transpose.o): > libcholmod.a(cholmod_l_triplet.o): > libcholmod.a(cholmod_l_check.o): > libcholmod.a(cholmod_l_read.o): > libcholmod.a(cholmod_l_write.o): > libcholmod.a(cholmod_l_amd.o): > libcholmod.a(cholmod_l_analyze.o): > libcholmod.a(cholmod_l_colamd.o): > libcholmod.a(cholmod_l_etree.o): > libcholmod.a(cholmod_l_factorize.o): > libcholmod.a(cholmod_l_postorder.o): > libcholmod.a(cholmod_l_rcond.o): > libcholmod.a(cholmod_l_resymbol.o): > libcholmod.a(cholmod_l_rowcolcounts.o): > libcholmod.a(cholmod_l_rowfac.o): > libcholmod.a(cholmod_l_solve.o): > libcholmod.a(cholmod_l_spsolve.o): > libcholmod.a(cholmod_l_drop.o): > libcholmod.a(cholmod_l_horzcat.o): > libcholmod.a(cholmod_l_norm.o): > libcholmod.a(cholmod_l_scale.o): > libcholmod.a(cholmod_l_sdmult.o): > libcholmod.a(cholmod_l_ssmult.o): > libcholmod.a(cholmod_l_submatrix.o): > libcholmod.a(cholmod_l_vertcat.o): > libcholmod.a(cholmod_l_symmetry.o): > libcholmod.a(cholmod_l_rowadd.o): > libcholmod.a(cholmod_l_rowdel.o): > libcholmod.a(cholmod_l_updown.o): > libcholmod.a(cholmod_l_super_numeric.o): > libcholmod.a(cholmod_l_super_solve.o): > libcholmod.a(cholmod_l_super_symbolic.o): > libcholmod.a(cholmod_l_ccolamd.o): > libcholmod.a(cholmod_l_csymamd.o): > libcholmod.a(cholmod_l_metis.o): > libcholmod.a(cholmod_l_nesdis.o): > libcholmod.a(cholmod_l_camd.o): > > > On 5/19/2012 8:22 PM, Daniel Russel wrote: >> I doubt things have ever been looked into for doing static compilation of isd with cholmod. One needs to figure out which libraries cholmod depends on and add them to the add_dependency call (when doing dynamic linking they are brought in automatically). To help us get started, you can do ldd on the cholmod dynamic lib (somehting like /usr/lib/libcholmod.so) and send the results (if you are in a mac, you need to run "otool -L " on the .dylib instead). That shows what libraries the dynamic lib brings in on your platform. If you don't need isd, just disbable it as I'm not sure we want to get this working unless really needed as it could be painful. >> >> On May 19, 2012, at 7:41 PM, Seung Joong Kim wrote: >> >>> Hi Yannick, >>> >>> Suddenly I have a problem in compiling the ISD module as follows. Do you have any idea what happens? I recently upgraded to OSX 10.7 Lion, hopefully that is not an issue.. Thanks a lot! >>> >>> Compiling shared build/src/imp_isd_config.cpp >>> Compiling modules/isd/bin/benchmark_gaussianprocess.cpp >>> Install file: "build/swig/IMP_isd.i" as "build/data/swig/IMP_isd.i" >>> Running swig on file build/swig/IMP_isd.i >>> /opt/local/bin/swig -castmode -interface _IMP_isd -DPySwigIterator=IMP_ISD_PySwigIterator -DSwigPyIterator=IMP_ISD_SwigPyIterator -python -c++ -naturalvar -fvirtual -Wextra -o /Users/sjkim/imp/trunk/build/src/IMP_isd_wrap.cpp-in -oh /Users/sjkim/imp/trunk/build/src/IMP_isd_wrap.h-in -Ibuild/swig -I/opt/local/include -I/usr/include -I/usr/local/include -I/Users/sjkim/imp/trunk/build/include -I/Users/sjkim/imp/trunk -DIMP_SWIG /Users/sjkim/imp/trunk/build/swig/IMP_isd.i >>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>> Install file: "build/src/IMP.isd.py" as "build/lib/IMP/isd/__init__.py" >>> Patching swig file build/src/IMP_isd_wrap.h >>> Patching swig file build/src/IMP_isd_wrap.cpp >>> Compiling shared build/src/IMP_isd_wrap.cpp >>> Linking Shared Library build/lib/libimp_isd.dylib >>> Undefined symbols for architecture x86_64: >>> "_dpotrf_", referenced from: >>> _r_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>> "_zpotrf_", referenced from: >>> _c_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>> _z_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>> ld: symbol(s) not found for architecture x86_64 >>> collect2: ld returned 1 exit status >>> scons: *** [build/lib/libimp_isd.dylib] Error 1 >>> scons: building terminated because of errors. >>> >>> - SJ >>> >>> -- >>> Seung Joong Kim, Ph.D. >>> >>> Postdoctoral Scholar, Andrej Sali group >>> Department of Bioengineering and Therapeutic Sciences >>> University of California at San Francisco (UCSF) >>> 1-217-649-2147 >>> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > -- > Seung Joong Kim, Ph.D. > > Postdoctoral Scholar, Andrej Sali group > Department of Bioengineering and Therapeutic Sciences > University of California at San Francisco (UCSF) > 1-217-649-2147 > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Unfortunately this option (CHOLMOD="no") does not seem to be working. There is no difference with / without this option

- SJ

On 5/20/2012 7:32 AM, Daniel Russel wrote: > You can add CHOLMOD="no" to your config to turn it off. > > > > On May 20, 2012, at 2:16 AM, Yannick Spillyannick@salilab.org wrote: > >> Cholmod is optional for isd, and also only deprecated stuff uses it. I'd force the config to compile without cholmod if I knew how. >> >> On 20 mai 2012, at 07:22, Seung Joong Kimsjkim@salilab.org wrote: >> >>> There is only one libchomod in my mac >>> >>> /opt/local/lib/libcholmod.a >>> >>> Here is the result of "otool -L". Not sure how much helpful this information is.. By the way, I need to enable the "ISD" module, since it is required by the "SAXS_merge" module... If there is no easy solution, I will stick to use the linux machine. Thanks a lot! >>> >>> [sjkim@MAC /opt/local/lib]$ otool -L libcholmod.a >>> Archive : libcholmod.a >>> libcholmod.a(cholmod_aat.o): >>> libcholmod.a(cholmod_add.o): >>> libcholmod.a(cholmod_band.o): >>> libcholmod.a(cholmod_change_factor.o): >>> libcholmod.a(cholmod_common.o): >>> libcholmod.a(cholmod_complex.o): >>> libcholmod.a(cholmod_copy.o): >>> libcholmod.a(cholmod_dense.o): >>> libcholmod.a(cholmod_error.o): >>> libcholmod.a(cholmod_factor.o): >>> libcholmod.a(cholmod_memory.o): >>> libcholmod.a(cholmod_sparse.o): >>> libcholmod.a(cholmod_transpose.o): >>> libcholmod.a(cholmod_triplet.o): >>> libcholmod.a(cholmod_check.o): >>> libcholmod.a(cholmod_read.o): >>> libcholmod.a(cholmod_write.o): >>> libcholmod.a(cholmod_amd.o): >>> libcholmod.a(cholmod_analyze.o): >>> libcholmod.a(cholmod_colamd.o): >>> libcholmod.a(cholmod_etree.o): >>> libcholmod.a(cholmod_factorize.o): >>> libcholmod.a(cholmod_postorder.o): >>> libcholmod.a(cholmod_rcond.o): >>> libcholmod.a(cholmod_resymbol.o): >>> libcholmod.a(cholmod_rowcolcounts.o): >>> libcholmod.a(cholmod_rowfac.o): >>> libcholmod.a(cholmod_solve.o): >>> libcholmod.a(cholmod_spsolve.o): >>> libcholmod.a(cholmod_drop.o): >>> libcholmod.a(cholmod_horzcat.o): >>> libcholmod.a(cholmod_norm.o): >>> libcholmod.a(cholmod_scale.o): >>> libcholmod.a(cholmod_sdmult.o): >>> libcholmod.a(cholmod_ssmult.o): >>> libcholmod.a(cholmod_submatrix.o): >>> libcholmod.a(cholmod_vertcat.o): >>> libcholmod.a(cholmod_symmetry.o): >>> libcholmod.a(cholmod_rowadd.o): >>> libcholmod.a(cholmod_rowdel.o): >>> libcholmod.a(cholmod_updown.o): >>> libcholmod.a(cholmod_super_numeric.o): >>> libcholmod.a(cholmod_super_solve.o): >>> libcholmod.a(cholmod_super_symbolic.o): >>> libcholmod.a(cholmod_ccolamd.o): >>> libcholmod.a(cholmod_csymamd.o): >>> libcholmod.a(cholmod_metis.o): >>> libcholmod.a(cholmod_nesdis.o): >>> libcholmod.a(cholmod_camd.o): >>> libcholmod.a(cholmod_l_aat.o): >>> libcholmod.a(cholmod_l_add.o): >>> libcholmod.a(cholmod_l_band.o): >>> libcholmod.a(cholmod_l_change_factor.o): >>> libcholmod.a(cholmod_l_common.o): >>> libcholmod.a(cholmod_l_complex.o): >>> libcholmod.a(cholmod_l_copy.o): >>> libcholmod.a(cholmod_l_dense.o): >>> libcholmod.a(cholmod_l_error.o): >>> libcholmod.a(cholmod_l_factor.o): >>> libcholmod.a(cholmod_l_memory.o): >>> libcholmod.a(cholmod_l_sparse.o): >>> libcholmod.a(cholmod_l_transpose.o): >>> libcholmod.a(cholmod_l_triplet.o): >>> libcholmod.a(cholmod_l_check.o): >>> libcholmod.a(cholmod_l_read.o): >>> libcholmod.a(cholmod_l_write.o): >>> libcholmod.a(cholmod_l_amd.o): >>> libcholmod.a(cholmod_l_analyze.o): >>> libcholmod.a(cholmod_l_colamd.o): >>> libcholmod.a(cholmod_l_etree.o): >>> libcholmod.a(cholmod_l_factorize.o): >>> libcholmod.a(cholmod_l_postorder.o): >>> libcholmod.a(cholmod_l_rcond.o): >>> libcholmod.a(cholmod_l_resymbol.o): >>> libcholmod.a(cholmod_l_rowcolcounts.o): >>> libcholmod.a(cholmod_l_rowfac.o): >>> libcholmod.a(cholmod_l_solve.o): >>> libcholmod.a(cholmod_l_spsolve.o): >>> libcholmod.a(cholmod_l_drop.o): >>> libcholmod.a(cholmod_l_horzcat.o): >>> libcholmod.a(cholmod_l_norm.o): >>> libcholmod.a(cholmod_l_scale.o): >>> libcholmod.a(cholmod_l_sdmult.o): >>> libcholmod.a(cholmod_l_ssmult.o): >>> libcholmod.a(cholmod_l_submatrix.o): >>> libcholmod.a(cholmod_l_vertcat.o): >>> libcholmod.a(cholmod_l_symmetry.o): >>> libcholmod.a(cholmod_l_rowadd.o): >>> libcholmod.a(cholmod_l_rowdel.o): >>> libcholmod.a(cholmod_l_updown.o): >>> libcholmod.a(cholmod_l_super_numeric.o): >>> libcholmod.a(cholmod_l_super_solve.o): >>> libcholmod.a(cholmod_l_super_symbolic.o): >>> libcholmod.a(cholmod_l_ccolamd.o): >>> libcholmod.a(cholmod_l_csymamd.o): >>> libcholmod.a(cholmod_l_metis.o): >>> libcholmod.a(cholmod_l_nesdis.o): >>> libcholmod.a(cholmod_l_camd.o): >>> >>> >>> On 5/19/2012 8:22 PM, Daniel Russel wrote: >>>> I doubt things have ever been looked into for doing static compilation of isd with cholmod. One needs to figure out which libraries cholmod depends on and add them to the add_dependency call (when doing dynamic linking they are brought in automatically). To help us get started, you can do ldd on the cholmod dynamic lib (somehting like /usr/lib/libcholmod.so) and send the results (if you are in a mac, you need to run "otool -L " on the .dylib instead). That shows what libraries the dynamic lib brings in on your platform. If you don't need isd, just disbable it as I'm not sure we want to get this working unless really needed as it could be painful. >>>> >>>> On May 19, 2012, at 7:41 PM, Seung Joong Kim wrote: >>>> >>>>> Hi Yannick, >>>>> >>>>> Suddenly I have a problem in compiling the ISD module as follows. Do you have any idea what happens? I recently upgraded to OSX 10.7 Lion, hopefully that is not an issue.. Thanks a lot! >>>>> >>>>> Compiling shared build/src/imp_isd_config.cpp >>>>> Compiling modules/isd/bin/benchmark_gaussianprocess.cpp >>>>> Install file: "build/swig/IMP_isd.i" as "build/data/swig/IMP_isd.i" >>>>> Running swig on file build/swig/IMP_isd.i >>>>> /opt/local/bin/swig -castmode -interface _IMP_isd -DPySwigIterator=IMP_ISD_PySwigIterator -DSwigPyIterator=IMP_ISD_SwigPyIterator -python -c++ -naturalvar -fvirtual -Wextra -o /Users/sjkim/imp/trunk/build/src/IMP_isd_wrap.cpp-in -oh /Users/sjkim/imp/trunk/build/src/IMP_isd_wrap.h-in -Ibuild/swig -I/opt/local/include -I/usr/include -I/usr/local/include -I/Users/sjkim/imp/trunk/build/include -I/Users/sjkim/imp/trunk -DIMP_SWIG /Users/sjkim/imp/trunk/build/swig/IMP_isd.i >>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>> Install file: "build/src/IMP.isd.py" as "build/lib/IMP/isd/__init__.py" >>>>> Patching swig file build/src/IMP_isd_wrap.h >>>>> Patching swig file build/src/IMP_isd_wrap.cpp >>>>> Compiling shared build/src/IMP_isd_wrap.cpp >>>>> Linking Shared Library build/lib/libimp_isd.dylib >>>>> Undefined symbols for architecture x86_64: >>>>> "_dpotrf_", referenced from: >>>>> _r_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>>>> "_zpotrf_", referenced from: >>>>> _c_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>>>> _z_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>>>> ld: symbol(s) not found for architecture x86_64 >>>>> collect2: ld returned 1 exit status >>>>> scons: *** [build/lib/libimp_isd.dylib] Error 1 >>>>> scons: building terminated because of errors. >>>>> >>>>> - SJ >>>>> >>>>> -- >>>>> Seung Joong Kim, Ph.D. >>>>> >>>>> Postdoctoral Scholar, Andrej Sali group >>>>> Department of Bioengineering and Therapeutic Sciences >>>>> University of California at San Francisco (UCSF) >>>>> 1-217-649-2147 >>>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> -- >>> Seung Joong Kim, Ph.D. >>> >>> Postdoctoral Scholar, Andrej Sali group >>> Department of Bioengineering and Therapeutic Sciences >>> University of California at San Francisco (UCSF) >>> 1-217-649-2147 >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev

Well, I switched back to OSX 10.6.8 Snow leopard (the backup I made yesterday before upgrading to Lion), and everything is working fine. I suspect something was broken when I upgrade to OSX Lion. It is weird though, since I reinstalled / recompiled MacPort after upgrading to Lion.

I'll keep Snow leopard for a while, so never mind about it for now. Thank you so much for all your supports!

- SJ

On 5/20/2012 11:21 AM, Daniel Russel wrote: > Sorry, my mistake, it is lower case: cholmod="no" > > On May 20, 2012, at 8:50 AM, Seung Joong Kim wrote: > >> Unfortunately this option (CHOLMOD="no") does not seem to be working. There is no difference with / without this option >> >> - SJ >> >> >> On 5/20/2012 7:32 AM, Daniel Russel wrote: >>> You can add CHOLMOD="no" to your config to turn it off. >>> >>> >>> >>> On May 20, 2012, at 2:16 AM, Yannick Spillyannick@salilab.org wrote: >>> >>>> Cholmod is optional for isd, and also only deprecated stuff uses it. I'd force the config to compile without cholmod if I knew how. >>>> >>>> On 20 mai 2012, at 07:22, Seung Joong Kimsjkim@salilab.org wrote: >>>> >>>>> There is only one libchomod in my mac >>>>> >>>>> /opt/local/lib/libcholmod.a >>>>> >>>>> Here is the result of "otool -L". Not sure how much helpful this information is.. By the way, I need to enable the "ISD" module, since it is required by the "SAXS_merge" module... If there is no easy solution, I will stick to use the linux machine. Thanks a lot! >>>>> >>>>> [sjkim@MAC /opt/local/lib]$ otool -L libcholmod.a >>>>> Archive : libcholmod.a >>>>> libcholmod.a(cholmod_aat.o): >>>>> libcholmod.a(cholmod_add.o): >>>>> libcholmod.a(cholmod_band.o): >>>>> libcholmod.a(cholmod_change_factor.o): >>>>> libcholmod.a(cholmod_common.o): >>>>> libcholmod.a(cholmod_complex.o): >>>>> libcholmod.a(cholmod_copy.o): >>>>> libcholmod.a(cholmod_dense.o): >>>>> libcholmod.a(cholmod_error.o): >>>>> libcholmod.a(cholmod_factor.o): >>>>> libcholmod.a(cholmod_memory.o): >>>>> libcholmod.a(cholmod_sparse.o): >>>>> libcholmod.a(cholmod_transpose.o): >>>>> libcholmod.a(cholmod_triplet.o): >>>>> libcholmod.a(cholmod_check.o): >>>>> libcholmod.a(cholmod_read.o): >>>>> libcholmod.a(cholmod_write.o): >>>>> libcholmod.a(cholmod_amd.o): >>>>> libcholmod.a(cholmod_analyze.o): >>>>> libcholmod.a(cholmod_colamd.o): >>>>> libcholmod.a(cholmod_etree.o): >>>>> libcholmod.a(cholmod_factorize.o): >>>>> libcholmod.a(cholmod_postorder.o): >>>>> libcholmod.a(cholmod_rcond.o): >>>>> libcholmod.a(cholmod_resymbol.o): >>>>> libcholmod.a(cholmod_rowcolcounts.o): >>>>> libcholmod.a(cholmod_rowfac.o): >>>>> libcholmod.a(cholmod_solve.o): >>>>> libcholmod.a(cholmod_spsolve.o): >>>>> libcholmod.a(cholmod_drop.o): >>>>> libcholmod.a(cholmod_horzcat.o): >>>>> libcholmod.a(cholmod_norm.o): >>>>> libcholmod.a(cholmod_scale.o): >>>>> libcholmod.a(cholmod_sdmult.o): >>>>> libcholmod.a(cholmod_ssmult.o): >>>>> libcholmod.a(cholmod_submatrix.o): >>>>> libcholmod.a(cholmod_vertcat.o): >>>>> libcholmod.a(cholmod_symmetry.o): >>>>> libcholmod.a(cholmod_rowadd.o): >>>>> libcholmod.a(cholmod_rowdel.o): >>>>> libcholmod.a(cholmod_updown.o): >>>>> libcholmod.a(cholmod_super_numeric.o): >>>>> libcholmod.a(cholmod_super_solve.o): >>>>> libcholmod.a(cholmod_super_symbolic.o): >>>>> libcholmod.a(cholmod_ccolamd.o): >>>>> libcholmod.a(cholmod_csymamd.o): >>>>> libcholmod.a(cholmod_metis.o): >>>>> libcholmod.a(cholmod_nesdis.o): >>>>> libcholmod.a(cholmod_camd.o): >>>>> libcholmod.a(cholmod_l_aat.o): >>>>> libcholmod.a(cholmod_l_add.o): >>>>> libcholmod.a(cholmod_l_band.o): >>>>> libcholmod.a(cholmod_l_change_factor.o): >>>>> libcholmod.a(cholmod_l_common.o): >>>>> libcholmod.a(cholmod_l_complex.o): >>>>> libcholmod.a(cholmod_l_copy.o): >>>>> libcholmod.a(cholmod_l_dense.o): >>>>> libcholmod.a(cholmod_l_error.o): >>>>> libcholmod.a(cholmod_l_factor.o): >>>>> libcholmod.a(cholmod_l_memory.o): >>>>> libcholmod.a(cholmod_l_sparse.o): >>>>> libcholmod.a(cholmod_l_transpose.o): >>>>> libcholmod.a(cholmod_l_triplet.o): >>>>> libcholmod.a(cholmod_l_check.o): >>>>> libcholmod.a(cholmod_l_read.o): >>>>> libcholmod.a(cholmod_l_write.o): >>>>> libcholmod.a(cholmod_l_amd.o): >>>>> libcholmod.a(cholmod_l_analyze.o): >>>>> libcholmod.a(cholmod_l_colamd.o): >>>>> libcholmod.a(cholmod_l_etree.o): >>>>> libcholmod.a(cholmod_l_factorize.o): >>>>> libcholmod.a(cholmod_l_postorder.o): >>>>> libcholmod.a(cholmod_l_rcond.o): >>>>> libcholmod.a(cholmod_l_resymbol.o): >>>>> libcholmod.a(cholmod_l_rowcolcounts.o): >>>>> libcholmod.a(cholmod_l_rowfac.o): >>>>> libcholmod.a(cholmod_l_solve.o): >>>>> libcholmod.a(cholmod_l_spsolve.o): >>>>> libcholmod.a(cholmod_l_drop.o): >>>>> libcholmod.a(cholmod_l_horzcat.o): >>>>> libcholmod.a(cholmod_l_norm.o): >>>>> libcholmod.a(cholmod_l_scale.o): >>>>> libcholmod.a(cholmod_l_sdmult.o): >>>>> libcholmod.a(cholmod_l_ssmult.o): >>>>> libcholmod.a(cholmod_l_submatrix.o): >>>>> libcholmod.a(cholmod_l_vertcat.o): >>>>> libcholmod.a(cholmod_l_symmetry.o): >>>>> libcholmod.a(cholmod_l_rowadd.o): >>>>> libcholmod.a(cholmod_l_rowdel.o): >>>>> libcholmod.a(cholmod_l_updown.o): >>>>> libcholmod.a(cholmod_l_super_numeric.o): >>>>> libcholmod.a(cholmod_l_super_solve.o): >>>>> libcholmod.a(cholmod_l_super_symbolic.o): >>>>> libcholmod.a(cholmod_l_ccolamd.o): >>>>> libcholmod.a(cholmod_l_csymamd.o): >>>>> libcholmod.a(cholmod_l_metis.o): >>>>> libcholmod.a(cholmod_l_nesdis.o): >>>>> libcholmod.a(cholmod_l_camd.o): >>>>> >>>>> >>>>> On 5/19/2012 8:22 PM, Daniel Russel wrote: >>>>>> I doubt things have ever been looked into for doing static compilation of isd with cholmod. One needs to figure out which libraries cholmod depends on and add them to the add_dependency call (when doing dynamic linking they are brought in automatically). To help us get started, you can do ldd on the cholmod dynamic lib (somehting like /usr/lib/libcholmod.so) and send the results (if you are in a mac, you need to run "otool -L " on the .dylib instead). That shows what libraries the dynamic lib brings in on your platform. If you don't need isd, just disbable it as I'm not sure we want to get this working unless really needed as it could be painful. >>>>>> >>>>>> On May 19, 2012, at 7:41 PM, Seung Joong Kim wrote: >>>>>> >>>>>>> Hi Yannick, >>>>>>> >>>>>>> Suddenly I have a problem in compiling the ISD module as follows. Do you have any idea what happens? I recently upgraded to OSX 10.7 Lion, hopefully that is not an issue.. Thanks a lot! >>>>>>> >>>>>>> Compiling shared build/src/imp_isd_config.cpp >>>>>>> Compiling modules/isd/bin/benchmark_gaussianprocess.cpp >>>>>>> Install file: "build/swig/IMP_isd.i" as "build/data/swig/IMP_isd.i" >>>>>>> Running swig on file build/swig/IMP_isd.i >>>>>>> /opt/local/bin/swig -castmode -interface _IMP_isd -DPySwigIterator=IMP_ISD_PySwigIterator -DSwigPyIterator=IMP_ISD_SwigPyIterator -python -c++ -naturalvar -fvirtual -Wextra -o /Users/sjkim/imp/trunk/build/src/IMP_isd_wrap.cpp-in -oh /Users/sjkim/imp/trunk/build/src/IMP_isd_wrap.h-in -Ibuild/swig -I/opt/local/include -I/usr/include -I/usr/local/include -I/Users/sjkim/imp/trunk/build/include -I/Users/sjkim/imp/trunk -DIMP_SWIG /Users/sjkim/imp/trunk/build/swig/IMP_isd.i >>>>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>>>> /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' >>>>>>> Install file: "build/src/IMP.isd.py" as "build/lib/IMP/isd/__init__.py" >>>>>>> Patching swig file build/src/IMP_isd_wrap.h >>>>>>> Patching swig file build/src/IMP_isd_wrap.cpp >>>>>>> Compiling shared build/src/IMP_isd_wrap.cpp >>>>>>> Linking Shared Library build/lib/libimp_isd.dylib >>>>>>> Undefined symbols for architecture x86_64: >>>>>>> "_dpotrf_", referenced from: >>>>>>> _r_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>>>>>> "_zpotrf_", referenced from: >>>>>>> _c_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>>>>>> _z_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) >>>>>>> ld: symbol(s) not found for architecture x86_64 >>>>>>> collect2: ld returned 1 exit status >>>>>>> scons: *** [build/lib/libimp_isd.dylib] Error 1 >>>>>>> scons: building terminated because of errors. >>>>>>> >>>>>>> - SJ >>>>>>> >>>>>>> -- >>>>>>> Seung Joong Kim, Ph.D. >>>>>>> >>>>>>> Postdoctoral Scholar, Andrej Sali group >>>>>>> Department of Bioengineering and Therapeutic Sciences >>>>>>> University of California at San Francisco (UCSF) >>>>>>> 1-217-649-2147 >>>>>>> >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> -- >>>>> Seung Joong Kim, Ph.D. >>>>> >>>>> Postdoctoral Scholar, Andrej Sali group >>>>> Department of Bioengineering and Therapeutic Sciences >>>>> University of California at San Francisco (UCSF) >>>>> 1-217-649-2147 >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> -- >> Seung Joong Kim, Ph.D. >> >> Postdoctoral Scholar, Andrej Sali group >> Department of Bioengineering and Therapeutic Sciences >> University of California at San Francisco (UCSF) >> 1-217-649-2147 >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev