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]
