Discussion on science-related applications and integration in Gentoo.

Janusz Mordarski | 5 Feb 2009 16:14

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Re: sys-cluster infiniband , mpi related soft. update request

Can you tell me which package from your openib ebuilds adds mlx4_ib 
module and other infiniband drivers? i installed whole openib package 
with mlx4 flag, but there's no mlx4_ib module since i removed it from 
kernel (i wanted to use OFED drivers, not those from kernel)

--

-- 
Dept of Computational Biophysics & Bioinformatics,
Faculty of Biochemistry, Biophysics and Biotechnology,
Jagiellonian University,
ul. Gronostajowa 7,
30-387 Krakow, Poland.
Tel: (+48-12)-664-6380

Janusz Mordarski | 5 Feb 2009 19:48

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Re: sys-cluster infiniband , mpi related soft. update request

Well ok i've made my own ebuild with openib-drivers , v 1.4 (in 
attachment), i tried it and it compiles except ehca flag (won't compile 
with it), if someone's interested, please check it and put into the overlay

i have another question, i have big PERFORMANCE problems with infiniband 
on gentoo, no matter if i use kernel drivers or openib-drivers, here's 
what OSU latency benchmark says:

first, OSU over Gigabit Ethernet (for comparison):
# OSU MPI Latency Test v3.1.1
# Size            Latency (us)
0                        76.37
1                        77.77
2                        77.66
4                        77.92
8                        77.95
16                       77.98

Infiniband - drivers from openib-drivers ebuild
# OSU MPI Latency Test v3.1.1
# Size            Latency (us)
0                        50.23
1                        52.10
2                        51.99
4                        51.62
8                        51.79
16                       52.17

Infiniband - drivers from kernel 2.6.27 - results are almost the same, 
except everywhere, where there is 5x (fifty) , it's 4x (fourty)

(Continue reading)

Reinis Danne | 6 Feb 2009 20:41

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[PATCH] sci-chemistry/ghemical: Added ghemical package

Added patches from #212689, #232292 and #246414 to ebuilds for ghemical-2.95 and 2.98.
---
 sci-chemistry/ghemical/ChangeLog                   |   18 +++++
 sci-chemistry/ghemical/Manifest                    |   12 +++
 .../files/ghemical-2.95-g_threads-246414.patch     |   26 +++++++
 .../files/ghemical-2.95-import_export-212689.patch |   54 ++++++++++++++
 .../ghemical-2.95-libf2c_config_test-232292.patch  |   13 ++++
 .../files/ghemical-2.98-import_export-212689.patch |   54 ++++++++++++++
 .../ghemical-2.98-libf2c_config_test-232292.patch  |   13 ++++
 sci-chemistry/ghemical/files/ghemical-gcc43.patch  |   14 ++++
 sci-chemistry/ghemical/ghemical-2.95.ebuild        |   74 ++++++++++++++++++++
 sci-chemistry/ghemical/ghemical-2.98.ebuild        |   74 ++++++++++++++++++++
 sci-chemistry/ghemical/metadata.xml                |   21 ++++++
 11 files changed, 373 insertions(+), 0 deletions(-)
 create mode 100644 sci-chemistry/ghemical/ChangeLog
 create mode 100644 sci-chemistry/ghemical/Manifest
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-g_threads-246414.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-import_export-212689.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.95-libf2c_config_test-232292.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.98-import_export-212689.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-2.98-libf2c_config_test-232292.patch
 create mode 100644 sci-chemistry/ghemical/files/ghemical-gcc43.patch
 create mode 100644 sci-chemistry/ghemical/ghemical-2.95.ebuild
 create mode 100644 sci-chemistry/ghemical/ghemical-2.98.ebuild
 create mode 100644 sci-chemistry/ghemical/metadata.xml

diff --git a/sci-chemistry/ghemical/ChangeLog b/sci-chemistry/ghemical/ChangeLog
new file mode 100644
index 0000000..012896a
--- /dev/null

(Continue reading)

Reinis Danne | 7 Feb 2009 14:21

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[PATCH] New package sci-chemistry/bkchem, #95178 (Thanks to Beda Kosata)

Updated ebuild based on author's provided and wrote metadata.xml.
---
 sci-chemistry/bkchem/ChangeLog            |   10 ++++++++
 sci-chemistry/bkchem/Manifest             |    4 +++
 sci-chemistry/bkchem/bkchem-0.12.5.ebuild |   37 +++++++++++++++++++++++++++++
 sci-chemistry/bkchem/metadata.xml         |   11 ++++++++
 4 files changed, 62 insertions(+), 0 deletions(-)
 create mode 100644 sci-chemistry/bkchem/ChangeLog
 create mode 100644 sci-chemistry/bkchem/Manifest
 create mode 100644 sci-chemistry/bkchem/bkchem-0.12.5.ebuild
 create mode 100644 sci-chemistry/bkchem/metadata.xml

diff --git a/sci-chemistry/bkchem/ChangeLog b/sci-chemistry/bkchem/ChangeLog
new file mode 100644
index 0000000..dd354ae
--- /dev/null
+++ b/sci-chemistry/bkchem/ChangeLog
 <at>  <at>  -0,0 +1,10  <at>  <at> 
+# ChangeLog for sci-chemistry/bkchem
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bkchem-0.12.5 (07 Feb 2009)
+
+  07 Feb 2009; Reinis Danne <rei4dan <at> gmail.com> +metadata.xml,
+  +bkchem-0.12.5.ebuild:
+  New package sci-chemistry/bkchem, #95178 (Thanks to Beda Kosata)
+
diff --git a/sci-chemistry/bkchem/Manifest b/sci-chemistry/bkchem/Manifest
new file mode 100644

(Continue reading)

Reinis Danne | 7 Feb 2009 15:36

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[PATCH] New package sci-chemistry/wxmacmolplt, #197131

New ebuild for wxmacmolplt-7.2.1, metadata.xml and a patch for Ming use.
---
 sci-chemistry/wxmacmolplt/ChangeLog                |   11 ++++++
 sci-chemistry/wxmacmolplt/Manifest                 |    5 +++
 .../wxmacmolplt/files/wxmacmolplt-7.2.1-ming.patch |   11 ++++++
 sci-chemistry/wxmacmolplt/metadata.xml             |   11 ++++++
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.2.1.ebuild |   39 ++++++++++++++++++++
 5 files changed, 77 insertions(+), 0 deletions(-)
 create mode 100644 sci-chemistry/wxmacmolplt/ChangeLog
 create mode 100644 sci-chemistry/wxmacmolplt/Manifest
 create mode 100644 sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.2.1-ming.patch
 create mode 100644 sci-chemistry/wxmacmolplt/metadata.xml
 create mode 100644 sci-chemistry/wxmacmolplt/wxmacmolplt-7.2.1.ebuild

diff --git a/sci-chemistry/wxmacmolplt/ChangeLog b/sci-chemistry/wxmacmolplt/ChangeLog
new file mode 100644
index 0000000..bf976cd
--- /dev/null
+++ b/sci-chemistry/wxmacmolplt/ChangeLog
 <at>  <at>  -0,0 +1,11  <at>  <at> 
+# ChangeLog for sci-chemistry/wxmacmolplt
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*wxmacmolplt-7.2.1 (07 Feb 2009)
+
+  07 Feb 2009; Reinis Danne <rei4dan <at> gmail.com>
+  +files/wxmacmolplt-7.2.1-ming.patch, +metadata.xml,
+  +wxmacmolplt-7.2.1.ebuild:
+  New package sci-chemistry/wxmacmolplt, #197131

(Continue reading)

Juan Aguado | 8 Feb 2009 19:06

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Re: octave forge

Hopefully GCC-4.3 is going to be stabilized soon. Is there any comment 
on this?

Reinis Danne | 12 Feb 2009 22:54

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[PATCH] sci-chemistry/openbabel-2.2.0-r1: New ebuild with doxyfile patch, #212212

Added use flags doc (install API documentation) and zlib.
---
 sci-chemistry/openbabel/ChangeLog                  |   11 +++
 sci-chemistry/openbabel/Manifest                   |    5 ++
 .../openbabel/files/openbabel-2.2.0-doxyfile.patch |   27 ++++++++
 sci-chemistry/openbabel/metadata.xml               |   15 ++++
 sci-chemistry/openbabel/openbabel-2.2.0-r1.ebuild  |   68 ++++++++++++++++++++
 5 files changed, 126 insertions(+), 0 deletions(-)
 create mode 100644 sci-chemistry/openbabel/ChangeLog
 create mode 100644 sci-chemistry/openbabel/Manifest
 create mode 100644 sci-chemistry/openbabel/files/openbabel-2.2.0-doxyfile.patch
 create mode 100644 sci-chemistry/openbabel/metadata.xml
 create mode 100644 sci-chemistry/openbabel/openbabel-2.2.0-r1.ebuild

diff --git a/sci-chemistry/openbabel/ChangeLog b/sci-chemistry/openbabel/ChangeLog
new file mode 100644
index 0000000..1ffe227
--- /dev/null
+++ b/sci-chemistry/openbabel/ChangeLog
 <at>  <at>  -0,0 +1,11  <at>  <at> 
+# ChangeLog for sci-chemistry/openbabel
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openbabel-2.2.0-r1 (10 Feb 2009)
+
+  10 Feb 2009; Reinis Danne <rei4dan <at> gmail.com>
+  +files/openbabel-2.2.0-doxyfile.patch, +metadata.xml,
+  +openbabel-2.2.0-r1.ebuild:
+  Added openbabel-2.2.0-r1.ebuild with a patch for doxyfile, #212212

(Continue reading)

Reinis Danne | 12 Feb 2009 22:55

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[PATCH] New package sci-chemistry/openbabel-perl, #212212

Ebuild, metadata.xml and a patch for Makefile.PL.
---
 sci-chemistry/openbabel-perl/ChangeLog             |   11 +++
 sci-chemistry/openbabel-perl/Manifest              |    5 +
 .../files/openbabel-perl-2.2.0-makefile.patch      |   25 ++++++
 sci-chemistry/openbabel-perl/metadata.xml          |   15 ++++
 .../openbabel-perl/openbabel-perl-2.2.0.ebuild     |   82 ++++++++++++++++++++
 5 files changed, 138 insertions(+), 0 deletions(-)
 create mode 100644 sci-chemistry/openbabel-perl/ChangeLog
 create mode 100644 sci-chemistry/openbabel-perl/Manifest
 create mode 100644 sci-chemistry/openbabel-perl/files/openbabel-perl-2.2.0-makefile.patch
 create mode 100644 sci-chemistry/openbabel-perl/metadata.xml
 create mode 100644 sci-chemistry/openbabel-perl/openbabel-perl-2.2.0.ebuild

diff --git a/sci-chemistry/openbabel-perl/ChangeLog b/sci-chemistry/openbabel-perl/ChangeLog
new file mode 100644
index 0000000..d33744b
--- /dev/null
+++ b/sci-chemistry/openbabel-perl/ChangeLog
 <at>  <at>  -0,0 +1,11  <at>  <at> 
+# ChangeLog for sci-chemistry/openbabel-perl
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openbabel-perl-2.2.0 (10 Feb 2009)
+
+  10 Feb 2009; Reinis Danne <rei4dan <at> gmail.com>
+  +files/openbabel-perl-2.2.0-makefile.patch, +metadata.xml,
+  +openbabel-perl-2.2.0.ebuild:
+  New package sci-chemistry/openbabel-perl, #212212

(Continue reading)

Reinis Danne | 12 Feb 2009 22:56

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[PATCH] New package sci-chemistry/openbabel-python, #212212

openbabel-python-2.2.0.ebuild and metadata.xml.
---
 sci-chemistry/openbabel-python/ChangeLog           |   10 +++
 sci-chemistry/openbabel-python/Manifest            |    4 +
 sci-chemistry/openbabel-python/metadata.xml        |   15 ++++
 .../openbabel-python/openbabel-python-2.2.0.ebuild |   70 ++++++++++++++++++++
 4 files changed, 99 insertions(+), 0 deletions(-)
 create mode 100644 sci-chemistry/openbabel-python/ChangeLog
 create mode 100644 sci-chemistry/openbabel-python/Manifest
 create mode 100644 sci-chemistry/openbabel-python/metadata.xml
 create mode 100644 sci-chemistry/openbabel-python/openbabel-python-2.2.0.ebuild

diff --git a/sci-chemistry/openbabel-python/ChangeLog b/sci-chemistry/openbabel-python/ChangeLog
new file mode 100644
index 0000000..47d5339
--- /dev/null
+++ b/sci-chemistry/openbabel-python/ChangeLog
 <at>  <at>  -0,0 +1,10  <at>  <at> 
+# ChangeLog for sci-chemistry/openbabel-python
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openbabel-python-2.2.0 (10 Feb 2009)
+
+  10 Feb 2009; Reinis Danne <rei4dan <at> gmail.com> +metadata.xml,
+  +openbabel-python-2.2.0.ebuild:
+  New package sci-chemistry/openbabel-python, #212212
+
diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest
new file mode 100644

(Continue reading)

Reinis Danne | 12 Feb 2009 22:56

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[PATCH] New package sci-chemistry/openbabel-ruby, #212212

openbabel-ruby-2.2.0.ebuild and metadata.xml.
---
 sci-chemistry/openbabel-ruby/ChangeLog             |   10 +++
 sci-chemistry/openbabel-ruby/Manifest              |    4 +
 sci-chemistry/openbabel-ruby/metadata.xml          |   15 +++++
 .../openbabel-ruby/openbabel-ruby-2.2.0.ebuild     |   61 ++++++++++++++++++++
 4 files changed, 90 insertions(+), 0 deletions(-)
 create mode 100644 sci-chemistry/openbabel-ruby/ChangeLog
 create mode 100644 sci-chemistry/openbabel-ruby/Manifest
 create mode 100644 sci-chemistry/openbabel-ruby/metadata.xml
 create mode 100644 sci-chemistry/openbabel-ruby/openbabel-ruby-2.2.0.ebuild

diff --git a/sci-chemistry/openbabel-ruby/ChangeLog b/sci-chemistry/openbabel-ruby/ChangeLog
new file mode 100644
index 0000000..33eae8c
--- /dev/null
+++ b/sci-chemistry/openbabel-ruby/ChangeLog
 <at>  <at>  -0,0 +1,10  <at>  <at> 
+# ChangeLog for sci-chemistry/openbabel-ruby
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openbabel-ruby-2.2.0 (10 Feb 2009)
+
+  10 Feb 2009; Reinis Danne <rei4dan <at> gmail.com> +metadata.xml,
+  +openbabel-ruby-2.2.0.ebuild:
+  New package sci-chemistry/openbabel-ruby, #212212
+
diff --git a/sci-chemistry/openbabel-ruby/Manifest b/sci-chemistry/openbabel-ruby/Manifest
new file mode 100644

(Continue reading)

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