Hi Loris, Frederic, My apologies. I had forgotten that I also manipulated the easyblock. I tend to be somewhat of a hacker and I play with things till they work. I'd be good at this job if I kept better track :)
<https://www.njit.edu/> Glenn (Gedaliah) Wolosh, Ph.D. Ass't Director Research Software and Cloud Computing Acad & Research Computing Systems [email protected] <mailto:[email protected]> • (973) 596-5437 <tel:(973) 596-5437> A Top 100 National University U.S. News & World Report > On Feb 15, 2022, at 9:43 AM, Loris Bennett <[email protected]> wrote: > > Hi Frédéric, > > Frédéric Wautelet <[email protected] > <mailto:[email protected]>> writes: > >> Hi Loris, >> >> I've encountered the same issue. A workaround is to edit the rosetta >> easyblock as follow: >> >> ... >> >> # (extract and) copy database, docs, demos (incl tutorials) and >> biotools (if it's there) >> >> self.log.debug("Looking for database...") >> if os.path.exists(os.path.join(self.cfg['start_dir'], 'main', >> 'database')): >> extract_and_copy(os.path.join('main', 'database') + '%s') >> elif os.path.exists(os.path.join(self.cfg['start_dir'], 'database')): >> extract_and_copy(os.path.join('database') + '%s') >> else: >> extract_and_copy('rosetta_database%s') >> >> extract_and_copy('demos%s', optional=True, symlinks=True) >> >> ... > > Apart from the change regarding the path, you also have some extra > logging which is not here: > > > https://github.com/easybuilders/easybuild-easyblocks/blob/develop/easybuild/easyblocks/r/rosetta.py > > <https://github.com/easybuilders/easybuild-easyblocks/blob/develop/easybuild/easyblocks/r/rosetta.py> > > Any chance of you submitting a Pull-Request for what you are using? > >> I still have issues with rpm generation since there are file names with >> quotes such like: >> >> database/chemical/residue_type_sets/fa_standard_pre_talaris2013/patches/carbohydrates/N-R-3'-hydroxybutyryl-3-amination.txt >> >> >> and FPM doesn't seem to like it... >> >> If you don't generate rpm, everything should be fine. > > To be honest, I hadn't realised that creating RPMs with EB was possible. > I can't quite see a use-case for me, but I assume there must be > situations where that is something someone might want to do. > > Cheers, > > Loris > >> Regards, >> Frédéric >> >> On 15/02/22 15:01, Loris Bennett wrote: >> >> Hi Glenn, hi Frédéric, >> >> I used the patch file that Frédéric sent and the patching was >> successful, so thanks for that. >> >> However, the installation fails at the end with: >> >> == FAILED: Installation ended unsuccessfully (build directory: >> /trinity/shared/easybuild/build/Rosetta/3.13/foss-2019a): build failed >> (first 300 chars): Neither source directory >> '/trinity/shared/easybuild/build/Rosetta/3.13/foss-2019a/ros >> etta_src_2021.16.61629_bundle/main/rosetta_database', nor source tarball >> >> '/trinity/shared/easybuild/build/Rosetta/3.13/foss-2019a/rosetta_src_2021.16.61629_bundle/main/rosetta_database3.13.tgz' >> found. (took 23 mins 27 secs) >> >> If I do >> >> tar -tzf rosetta_src_3.13_bundle.tgz | grep 'main/rosetta_database' >> >> there is no such path. >> >> So it looks like I have to download the database separately. If so, >> where do I find it? >> >> Cheers, >> >> Loris >> >> "Glenn (Gedaliah) Wolosh" <[email protected]> writes: >> >> Hi Loris, >> >> [easybuild@node481 rosetta_src_2021.16.61629_bundle]$ pwd >> /home/e/easybuild/.local/easybuild/build/Rosetta/3.13/foss-2019a/rosetta_src_2021.16.61629_bundle >> [easybuild@node481 rosetta_src_2021.16.61629_bundle]$ patch -p1 < >> ~/.local/easybuild/sources/r/Rosetta/no.libxml2.build.patch >> patching file main/source/projects.settings >> patching file main/source/tools/build/basic.settings >> patching file main/source/tools/build/site.settings >> >> I believe this is how easybuild applies a patch. >> >> NJIT logo Glenn (Gedaliah) Wolosh, Ph.D. >> Ass't Director Research Software and Cloud Computing >> Acad & Research Computing Systems >> [email protected] • (973) 596-5437 >> >> A Top 100 National University >> U.S. News & World Report >> NJIT logo >> >> On Feb 14, 2022, at 8:32 AM, Loris Bennett <[email protected]> >> wrote: >> >> Hi Glenn, >> >> I have just tried out this patch, but it fails with >> >> Hunk #1 FAILED at 57. >> 1 out of 1 hunk FAILED -- saving rejects to file >> source/projects.settings.rej >> >> I have tried extracting projects.setting from the tarball and applying >> the patch directly but I then get >> >> [build@admin source]$ patch -l projects.settings ~/tmp/test.patch >> >> patching file projects.settings >> patching file projects.settings >> Hunk #1 FAILED at 153. >> Hunk #2 FAILED at 164. >> Hunk #3 FAILED at 1373. >> Hunk #4 FAILED at 1383. >> Hunk #5 FAILED at 2002. >> Hunk #6 FAILED at 2012. >> 6 out of 6 hunks FAILED -- saving rejects to file projects.settings.rej >> patching file projects.settings >> Hunk #1 FAILED at 28. >> 1 out of 1 hunk FAILED -- saving rejects to file projects.settings.rej >> >> I thought maybe the whitespace had been messed up when I copied the >> patch from the posting, but using --ignore-whitespace doesn't help. >> >> Any ideas what I might be doing wrong? >> >> Cheers, >> >> Loris >> >> "Glenn (Gedaliah) Wolosh" <[email protected]> writes: >> >> This easyconfig: >> name = 'Rosetta' >> version = '3.13' >> >> homepage = 'https://www.rosettacommons.org' >> description = """Rosetta is the premier software suite for modeling >> macromolecular structures. As a flexible, >> multi-purpose application, it includes tools for structure prediction, >> design, and remodeling of proteins and >> nucleic acids.""" >> >> toolchain = {'name': 'foss', 'version': '2019b'} >> toolchainopts = {'usempi': True} >> >> sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] >> >> patches = ['no.libxml2.build.patch'] >> >> moduleclass = 'bio' >> >> --------------------------------- >> >> This patch: >> diff -urNb rosetta_src_2021.16.61629_bundle/main/source/projects.settings >> rosetta_src_2021.16.61629_bundle_new/main/source/projects.settings >> --- rosetta_src_2021.16.61629_bundle/main/source/projects.settings >> 2021-04-20 16:48:40.000000000 -0400 >> +++ rosetta_src_2021.16.61629_bundle_new/main/source/projects.settings >> 2022-02-03 14:59:11.546839000 -0500 >> @@ -57,7 +57,6 @@ >> "cppdb", # Must come before sqlite3 for static build >> "sqlite3", >> "cifparse", >> - "libxml2", >> "libzmq", >> "rdkit", >> ] >> diff -urNb >> rosetta_src_2021.16.61629_bundle/main/source/tools/build/basic.settings >> rosetta_src_2021.16.61629_bundle_new/main/source/tools/build/basic.settings >> --- rosetta_src_2021.16.61629_bundle/main/source/tools/build/basic.settings >> 2021-04-20 16:58:07.000000000 -0400 >> +++ >> rosetta_src_2021.16.61629_bundle_new/main/source/tools/build/basic.settings >> 2022-02-03 16:41:20.569433000 -0500 >> @@ -153,7 +153,6 @@ >> "isystem external/", >> "isystem external/include/", >> "isystem external/dbio/", >> - "isystem external/libxml2/include", >> "isystem external/rdkit", >> ], >> "cxx" : [ >> @@ -164,7 +163,6 @@ >> "isystem external/", >> "isystem external/include/", >> "isystem external/dbio/", >> - "isystem external/libxml2/include", >> "isystem external/rdkit", >> >> #"fno-omit-frame-pointer", # -- useful for profiling on >> linux using RotateRight's Zoom profiler >> @@ -1373,7 +1371,6 @@ >> "isystem external/", >> "isystem external/include/", >> "isystem external/dbio/", >> - "isystem external/libxml2/include", >> "isystem external/rdkit", >> ], >> "cxx" : [ >> @@ -1383,7 +1380,6 @@ >> "isystem external/", >> "isystem external/include/", >> "isystem external/dbio/", >> - "isystem external/libxml2/include", >> "isystem external/rdkit", >> ], >> "warn" : [ >> @@ -2002,7 +1998,6 @@ >> "isystem external/", >> "isystem external/include/", >> "isystem external/dbio/", >> - "isystem external/libxml2/include", >> "isystem external/rdkit", >> ], >> "cxx" : [ >> @@ -2012,7 +2007,6 @@ >> "isystem external/", >> "isystem external/include/", >> "isystem external/dbio/", >> - "isystem external/libxml2/include", >> "isystem external/rdkit", >> ], >> "compile" : [ >> diff -urNb >> rosetta_src_2021.16.61629_bundle/main/source/tools/build/site.settings >> rosetta_src_2021.16.61629_bundle_new/main/source/tools/build/site.settings >> --- rosetta_src_2021.16.61629_bundle/main/source/tools/build/site.settings >> 2021-04-20 16:58:07.000000000 -0400 >> +++ >> rosetta_src_2021.16.61629_bundle_new/main/source/tools/build/site.settings >> 2022-02-03 16:45:31.839408000 -0500 >> @@ -28,6 +28,9 @@ >> "include_path" : os.environ["INCLUDE"].split(":") if "INCLUDE" >> in os.environ else [], >> }, >> "appends" : { >> + "flags" : { >> + "link" : ["lxml2"], >> + }, >> }, >> "overrides" : { >> ## Uncomment the following line if your compiler need additional environment >> variables to function (e.g. license key locations) >> >> NJIT logo Glenn (Gedaliah) Wolosh, Ph.D. >> Ass't Director Research Software and Cloud Computing >> Acad & Research Computing Systems >> [email protected] • (973) 596-5437 >> >> A Top 100 National University >> U.S. News & World Report >> NJIT logo >> >> On Feb 11, 2022, at 7:10 AM, Frédéric Wautelet <[email protected]> >> wrote: >> >> Hi, >> >> I also encountered this error. Could you please explain how you managed to >> disable libxml2? >> >> Thank you. >> >> With best regards, >> Frédéric Wautelet >> >> On 4/02/22 17:57, Glenn (Gedaliah) Wolosh wrote: >> >> I was able to disable the internal libxml2. Problem resolved. Thanks >> >> -- >> <Tv1z61Nf2bZCe6o6.png> >> >> Frédéric WAUTELET >> HPC Operations Engineer >> Faculty of Sciences >> >> T. +32(0)81725459 >> [email protected] >> http://www.ptci.unamur.be >> >> Université de Namur ASBL >> Rue de Bruxelles 61 - 5000 Namur >> Belgique >> >> Let’s respect the environment together. >> Only print this message if necessary! >> >> -- >> Dr. Loris Bennett (Herr/Mr) >> ZEDAT, Freie Universität Berlin Email [email protected] > -- > Dr. Loris Bennett (Herr/Mr) > ZEDAT, Freie Universität Berlin Email [email protected] > <mailto:[email protected]>
