Hi Frédéric,
Frédéric Wautelet <[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
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]
