arpack-ng #451

wpoely86 · 2013-10-04T09:10:53Z

Currently only the non-mpi version. The MPI version gives errors.

wpoely86 · 2013-10-04T11:00:06Z

MPI version works.

fgeorgatos · 2013-10-05T15:49:35Z

Job well done!

This may resolve partially or fully (see the tables where applicable):
easybuilders/easybuild-easyblocks#85
easybuilders/easybuild-easyblocks#86
easybuilders/easybuild-easyblocks#97 # arpack-only oriented
easybuilders/easybuild-easyblocks#111

Thanks @wpoely86 !

…r than one for a Clang-based toolchain)

…tions in toolchain easyconfigs

fix remarks

… toolchain

add gzip easyconfig for gmpolf toolchain, clean up comments in gmpolf toolchain

add easyconfigs for gmpolf toolchain + example easyconfig for gzip with gmpolf

Conflicts: setup.py

tloizou · 2013-10-24T14:22:02Z

Please check my pull request (#481). I have some additions in the patch file.

wpoely86 · 2013-10-24T14:34:03Z

@tloizou thanks for the additions to the patch file. The permanent fix is already upstream ( http://forge.scilab.org/index.php/p/arpack-ng/issues/1321/ ). It boils down to using an old version of libtool. I'm going to pull the upstream changes as a patch. That will give a large patch but will fix the issue permanently for everybody.

btw, You can also issue a pull request to my branch instead of a PR to the easyconfig repo. In that way, we can merge both our changes in 1 PR to easyconfig. That should make the life of @boegel a bit easier 😉

The autotools have been updated to the latest versions. This should fix a problem with intel MPI not being recognized by the configure scripts.

There are now 3 patches: one to bring arpack-ng to the current git HEAD (this is needed for the autotools update patch), one to update autotools (and fix all MPI issues) and one to update pkg-config.in file

…ild-easyconfigs into arpack-ng * 'contrib_arpack_ng' of https://github.com/tloizou/easybuild-easyconfigs: (46 commits) Change in config file Making changes in arpack-ng Adding arpack-ng Adding arpack-ng fix typo update release notes for EasyBuild v1.8.2 port thread pool patch to PSI 4.0b4, and use it to fix 'hanging' tests add gzip easyconfig for gmpolf toolchain, clean up comments in gmpolf toolchain fix final remarks align gmpich2 and gmpolf toolchain versions, fix dependency specifications in toolchain easyconfigs rebase gmpich easyconfig for FFTW 3.3.3 on gmvapich easyconfig (rather than one for a Clang-based toolchain) bump version to 1.9.0.0dev add PR easybuilders#462 to release notes, fix typo fix easyconfig file names w.r.t version suffixes bump version to v1.8.1.0, update release notes correct version to v1.8.1.0 PSI: avoid duplicate patch remove respecifying default max_fail_ratio of 0.5 in NWChem easyconfig really fix typo in patch file fix typo in patch file ... Conflicts: easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-configure-mpi.patch

wpoely86 · 2013-11-04T10:05:46Z

I've updated things a bit. We now patch to the latest git HEAD so we can use the upstream patch for autotools. This should fix all issues with Intel MPI. I've split it up into three patches (see the commit messages).

@tloizou I've pulled in your PR (#481), and changed some things. Can you check if everything still works for you?

As a result, some unrelated commits have been added as @tloizou branch was branched off after my branch. I hope this is now problem for you @boegel ?

hpcugentbot · 2013-11-07T10:35:44Z

Automatic reply from Jenkins: Can I test this?

boegel · 2013-11-11T18:09:49Z

Jenkins: ok to test

boegel · 2013-11-11T18:15:45Z

easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb

+configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.so", "lib/libparpack.a", "lib/libarpack.a"],


lib/libarpack.a is checked twice, once is good enough ;)

It should be libparpack.so, fixed in latest commit.

boegel · 2013-11-11T18:35:48Z

@wpoely86: The list of patches for the MPI versions doesn't work (the -mt build is OK), even without touching the order... I guess you including a full-blown patch for configure rather than a minimal one broke stuff.

== 2013-11-11 19:27:49,804 main.filetools ERROR EasyBuild crashed with an error
(at easybuild/tools/filetools.py:700 in parse_cmd_output):
cmd "patch -b -p1 -i <path>/arpack-ng-3.1.3-configure-mpi.patch" exited with exitcode 1 and output:
...
patching file m4/libtool.m4
patching file m4/ltoptions.m4
patching file missing
patching file compile
The next patch would create the file compile,
which already exists!  Assume -R? [n] 
Apply anyway? [n] 
Skipping patch.
1 out of 1 hunk ignored

Also, I rather prefer the minimal patch that @tloizou was using, since it makes it a lot more clear what's going on exactly...

What's the update-to-head patch about? Is that only bug fixes? Maybe that should be reflected by a version suffix like -patched or somesuch, since this build is not a clean 3.1.3?

wpoely86 · 2013-11-11T19:28:36Z

The reason the patch is so big, is that I updated autotools to their latest version. This fixes the MPI problem for everybody. I had to patch something to get MPI working, @tloizou needed something patched too, ... These patches are big but fix the problem for all cases. But maybe I should make a version of my own arpack-ng-20131111-ictce-5.5.0.eb or so.

It's very strange that these patches fail for you. They apply cleanly here. Are you testing arpack-ng-3.1.3-ictce-5.5.0.eb? It complains about the file compile existing already but If I look in the tarball, it isn't there?

boegel · 2013-11-11T19:36:57Z

@wpoely86: The patch issue must be because of a difference in the version of the patch command (I have version 2.6)...

The problem seems to come from the patch itself: it effectively has two blocks for creating the compile file. The first is at lines 383-390, the second at 3863-... The second block first deletes the existing file, which is where it goes wrong probably. Let me try and fix it (I love editing patch files :P).

wpoely86 · 2013-11-11T19:40:11Z

compile should be a symlink, so it should be easy.

Btw, patch 2.7.1 FTW 😉

boegel · 2013-11-11T19:43:10Z

compile should be a symlink? to what? the patch file doesn't suggest it's a symlink...

wpoely86 · 2013-11-11T19:46:30Z

oeps, it was a symlink and that was wrong. The patch first creates a symlink, then deletes, and fills in the file. The first two steps can be skipped. Do you fix it or should I do it?

boegel · 2013-11-11T19:50:38Z

@wpoely86: Fixed in wpoely86#8

boegel · 2013-11-11T19:51:00Z

Can you retest the build with the adjusted patch on your end?

wpoely86 · 2013-11-11T19:51:56Z

build works on my end.

boegel · 2013-11-11T20:18:19Z

Merging in, thanks @wpoely86!

arpack-ng

wpoely86 added 2 commits October 4, 2013 11:04

Added arpack-ng-3.1.3 with ictce-5.5.0 without MPI

cb03391

Added arpack-ng-3.1.3 with ictce-5.5.0 with MPI

324c5f9

wpoely86 and others added 15 commits October 7, 2013 13:29

arpack-ng: fixed incorrect lib in pkg-config file

a2887c3

Adding all eb config files for the new gmpolf toolchain.

5f03bc4

bump version to 1.9.0.0dev

c9feb0b

rebase gmpich easyconfig for FFTW 3.3.3 on gmvapich easyconfig (rathe…

a4bb27b

…r than one for a Clang-based toolchain)

align gmpich2 and gmpolf toolchain versions, fix dependency specifica…

9384e92

…tions in toolchain easyconfigs

fix final remarks

6fd3a5d

Merge pull request #1 from boegel/adding_gmpolf

40ca624

fix remarks

add gzip easyconfig for gmpolf toolchain, clean up comments in gmpolf…

7fa61c0

… toolchain

Merge pull request #2 from boegel/adding_gmpolf

8b4b02d

add gzip easyconfig for gmpolf toolchain, clean up comments in gmpolf toolchain

Merge pull request easybuilders#460 from Bart-CER/adding_gmpolf

c867fc1

add easyconfigs for gmpolf toolchain + example easyconfig for gzip with gmpolf

Merge branch 'v1.8.0.x' into develop

808a471

Merge branch 'v1.8.0.x' into develop

6222e4f

Conflicts: setup.py

Adding arpack-ng

f8cd200

Adding arpack-ng

bf94401

Making changes in arpack-ng

b6f9445

Thekla and others added 7 commits October 24, 2013 17:46

Change in config file

1f21738

arpack-ng: fixed typo

928a649

arpack-ng: updated the configure script patch to upstream patch

03ff0cb

The autotools have been updated to the latest versions. This should fix a problem with intel MPI not being recognized by the configure scripts.

arpack-ng: reorded patches

9bc79b0

There are now 3 patches: one to bring arpack-ng to the current git HEAD (this is needed for the autotools update patch), one to update autotools (and fix all MPI issues) and one to update pkg-config.in file

arpack-ng: added libparpack to sanity check

cd6fb5b

arpack-ng: updated patches for ictce-5.3 build

03e58ff

wpoely86 mentioned this pull request Nov 4, 2013

Contrib arpack ng #481

Merged

boegel reviewed Nov 11, 2013
View reviewed changes

arpack-ng: correct sanity files list

a522b7b

fix arpack-ng patch file

35889c2

boegel added a commit that referenced this pull request Nov 11, 2013

Merge pull request #451 from wpoely86/arpack-ng

9623746

arpack-ng

boegel merged commit 9623746 into easybuilders:develop Nov 11, 2013

wpoely86 deleted the arpack-ng branch November 11, 2013 20:18

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arpack-ng #451

arpack-ng #451

wpoely86 commented Oct 4, 2013

wpoely86 commented Oct 4, 2013

fgeorgatos commented Oct 5, 2013

tloizou commented Oct 24, 2013

wpoely86 commented Oct 24, 2013

wpoely86 commented Nov 4, 2013

hpcugentbot commented Nov 7, 2013

boegel commented Nov 11, 2013

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wpoely86 Nov 11, 2013

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arpack-ng #451

arpack-ng #451

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wpoely86 commented Oct 4, 2013

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