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 protected]
