[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Dominik 'Rathann' Mierzejewski changed: What|Removed |Added Blocks|505154 (FE-SCITECH) | Referenced Bugs: https://bugzilla.redhat.com/show_bug.cgi?id=505154 [Bug 505154] Tracker: Review Requests for Science and Technology related packages -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Fedora Update System changed: What|Removed |Added Fixed In Version|nwchem-6.3.2-9.fc20 |nwchem-6.3.2-9.el6 --- Comment #37 from Fedora Update System --- nwchem-6.3.2-9.el6 has been pushed to the Fedora EPEL 6 stable repository. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Fedora Update System changed: What|Removed |Added Status|ON_QA |CLOSED Fixed In Version||nwchem-6.3.2-9.fc20 Resolution|--- |ERRATA Last Closed||2014-04-26 05:22:04 --- Comment #36 from Fedora Update System --- nwchem-6.3.2-9.fc20 has been pushed to the Fedora 20 stable repository. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #35 from Fedora Update System --- nwchem-6.3.2-9.fc20 has been submitted as an update for Fedora 20. https://admin.fedoraproject.org/updates/nwchem-6.3.2-9.fc20 -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #34 from Fedora Update System --- nwchem-6.3.2-9.el6 has been submitted as an update for Fedora EPEL 6. https://admin.fedoraproject.org/updates/nwchem-6.3.2-9.el6 -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Bug 984605 depends on bug 1081403, which changed state. Bug 1081403 Summary: enable --enable-peigs https://bugzilla.redhat.com/show_bug.cgi?id=1081403 What|Removed |Added Status|ON_QA |CLOSED Resolution|--- |ERRATA -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Bug 984605 depends on bug 1081404, which changed state. Bug 1081404 Summary: Update ga to at least 5.3b (present on Fedora 21) https://bugzilla.redhat.com/show_bug.cgi?id=1081404 What|Removed |Added Status|ON_QA |CLOSED Resolution|--- |ERRATA -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 marcindulak changed: What|Removed |Added Depends On||1081404 Referenced Bugs: https://bugzilla.redhat.com/show_bug.cgi?id=1081404 [Bug 1081404] Update ga to at least 5.3b (present on Fedora 21) -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 marcindulak changed: What|Removed |Added Depends On||1081403 Referenced Bugs: https://bugzilla.redhat.com/show_bug.cgi?id=1081403 [Bug 1081403] enable --enable-peigs -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Bug 984605 depends on bug 1037075, which changed state. Bug 1037075 Summary: ga FTBFS if "-Werror=format-security" flag is used https://bugzilla.redhat.com/show_bug.cgi?id=1037075 What|Removed |Added Status|NEW |CLOSED Resolution|--- |RAWHIDE -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 marcindulak changed: What|Removed |Added Depends On||1037075 Referenced Bugs: https://bugzilla.redhat.com/show_bug.cgi?id=1037075 [Bug 1037075] ga FTBFS if "-Werror=format-security" flag is used -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Fedora Update System changed: What|Removed |Added Status|MODIFIED|ON_QA --- Comment #33 from Fedora Update System --- nwchem-6.3.2-7.el6 has been pushed to the Fedora EPEL 6 testing repository. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #32 from Fedora Update System --- nwchem-6.3.2-7.fc19 has been submitted as an update for Fedora 19. https://admin.fedoraproject.org/updates/nwchem-6.3.2-7.fc19 -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #31 from Fedora Update System --- nwchem-6.3.2-7.fc20 has been submitted as an update for Fedora 20. https://admin.fedoraproject.org/updates/nwchem-6.3.2-7.fc20 -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #30 from Fedora Update System --- nwchem-6.3.2-7.el6 has been submitted as an update for Fedora EPEL 6. https://admin.fedoraproject.org/updates/nwchem-6.3.2-7.el6 -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Fedora Update System changed: What|Removed |Added Status|ASSIGNED|MODIFIED -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #29 from Jon Ciesla --- Git done (by process-git-requests). -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Jon Ciesla changed: What|Removed |Added Flags|fedora-cvs? |fedora-cvs+ -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 marcindulak changed: What|Removed |Added Flags||fedora-cvs? --- Comment #28 from marcindulak --- New Package SCM Request === Package Name: nwchem Short Description: Delivering High-Performance Computational Chemistry to Science Owners: marcindulak Branches: f19 f20 el6 epel7 InitialCC: -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Antonio Trande changed: What|Removed |Added Flags|fedora-review? |fedora-review+ --- Comment #27 from Antonio Trande --- Package approved. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #26 from marcindulak --- (In reply to Antonio Trande from comment #24) > - 'common' subpackage contains data files and should be a 'noarch' package OK now > - License file is missing if you don't install basic package (nwchem). >Add '%doc LICENSE.txt' to %files in nwchem-common OK now > - '/etc/profile.d' directory is owned by 'setup' package. Please, list all > files > installed within it explicitely i think this request is just for readability - nwchem does not own /etc/profile.d, so i changed the * glob to a more readable one. /etc/profile.d files are now %config(noreplace) - just in case someone edits the files to set some additional nwchem variables > - ExcludeArch tag issue: the ARM package is not built (see comment#22) OK now > - Many tests are not passed. Decide if it's convenient for you to execute > them or not. i keep the tests as is. Failed tests is clearly an indication that something is wrong, and i see more of failed tests on i686. For example tests/h2o_opt/h2o_opt fails on Rawhide i686 at so called "geometry optimization" - looks like some numerical problems. The same test passes on EPEL6 i686, or on Fedora 20 x86_64. > - Please, fix the 'summary-too-long' errors. OK now > > Additional notes: > > - newchem building does not use all OPTFLAGS requested by Fedora Packaging > Guidelines because > they seem compromise the software functionalities; upstream maintainers said > in > INSTALL file: > >"The basic build tries to optimize NWChem for most systems and >most operating systems. Therefore, possible optimizations have >been excluded." > > - nwchem compiles/uses but does not distribute managed/optimized versions of > GA package. > > Package Review > == > > Legend: > [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated > [ ] = Manual review needed > > > > = MUST items = > > C/C++: > [x]: Package does not contain kernel modules. > [x]: Package contains no static executables. > [x]: Package does not contain any libtool archives (.la) > [x]: Rpath absent or only used for internal libs. > > Generic: > [x]: Package is licensed with an open-source compatible license and meets > other legal requirements as defined in the legal section of Packaging > Guidelines. > [x]: License field in the package spec file matches the actual license. > Note: Checking patched sources after %prep for licenses. Licenses found: > "GPL (v2 or later)", "Unknown or generated", "BSD (4 clause)", "LGPL (v2 > or later) (with incorrect FSF address)", "*No copyright* Public domain", > "BSD (3 clause)", "BSD (2 clause)". 4064 files have unknown license. > Detailed output of licensecheck in > /home/sagitter/nwchem/licensecheck.txt > [!]: License file installed when any subpackage combination is installed. > [!]: Package must own all directories that it creates. > Note: Directories without known owners: /etc/profile.d > [?]: %build honors applicable compiler flags or justifies otherwise. > [x]: Package contains no bundled libraries without FPC exception. > [x]: Changelog in prescribed format. > [x]: Sources contain only permissible code or content. > [-]: Package contains desktop file if it is a GUI application. > [-]: Development files must be in a -devel package > [x]: Package uses nothing in %doc for runtime. > [x]: Package consistently uses macros (instead of hard-coded directory > names). > [x]: Package is named according to the Package Naming Guidelines. > [x]: Package does not generate any conflict. > [x]: Package obeys FHS, except libexecdir and /usr/target. > [-]: If the package is a rename of another package, proper Obsoletes and > Provides are present. > [x]: Requires correct, justified where necessary. > [x]: Spec file is legible and written in American English. > [-]: Package contains systemd file(s) if in need. > [x]: Useful -debuginfo package or justification otherwise. > [!]: Package is not known to require an ExcludeArch tag. > [x]: Large documentation must go in a -doc subpackage. Large could be size > (~1MB) or number of files. > Note: Documentation size is 10240 bytes in 1 files. > [!]: Package complies to the Packaging Guidelines > [x]: Package successfully compiles and builds into binary rpms on at least > one > supported primary architecture. > [x]: Package installs properly. > [x]: Rpmlint is run on all rpms the build produces. > Note: There are rpmlint messages (see attachment). > [x]: If (and only if) the source package includes the text of the license(s) > in its own file, then that file, containing the text of the license(s) > for the package is included in %doc. > [x]: Package requires other packages for directories it uses. > [x]: Package does not own files or directories owned by other packages. > [x]: All build dependencies are listed in BuildRequires, except for any that > are
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #25 from Antonio Trande --- (In reply to marcindulak from comment #23) > GA is FTBFS on ARM bug #964424 . By they way i think that bug should also > have Blocks: F-ExcludeArch-arm > > For the moment i placed that bug in the nwchem.spec file comment. > > Spec URL: http://marcindulak.fedorapeople.org/packages/nwchem/r05/nwchem.spec > SRPM URL: > http://marcindulak.fedorapeople.org/packages/nwchem/r05/nwchem-6.3.2-5.fc21. > src.rpm Excuse me, I had not read your latest comment yet. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605
--- Comment #24 from Antonio Trande ---
- 'common' subpackage contains data files and should be a 'noarch' package
- License file is missing if you don't install basic package (nwchem).
Add '%doc LICENSE.txt' to %files in nwchem-common
- '/etc/profile.d' directory is owned by 'setup' package. Please, list all
files
installed within it explicitely
- ExcludeArch tag issue: the ARM package is not built (see comment#22)
- Many tests are not passed. Decide if it's convenient for you to execute them
or not.
- Please, fix the 'summary-too-long' errors.
Additional notes:
- newchem building does not use all OPTFLAGS requested by Fedora Packaging
Guidelines because
they seem compromise the software functionalities; upstream maintainers said in
INSTALL file:
"The basic build tries to optimize NWChem for most systems and
most operating systems. Therefore, possible optimizations have
been excluded."
- nwchem compiles/uses but does not distribute managed/optimized versions of GA
package.
Package Review
==
Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed
= MUST items =
C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[x]: Package does not contain any libtool archives (.la)
[x]: Rpath absent or only used for internal libs.
Generic:
[x]: Package is licensed with an open-source compatible license and meets
other legal requirements as defined in the legal section of Packaging
Guidelines.
[x]: License field in the package spec file matches the actual license.
Note: Checking patched sources after %prep for licenses. Licenses found:
"GPL (v2 or later)", "Unknown or generated", "BSD (4 clause)", "LGPL (v2
or later) (with incorrect FSF address)", "*No copyright* Public domain",
"BSD (3 clause)", "BSD (2 clause)". 4064 files have unknown license.
Detailed output of licensecheck in /home/sagitter/nwchem/licensecheck.txt
[!]: License file installed when any subpackage combination is installed.
[!]: Package must own all directories that it creates.
Note: Directories without known owners: /etc/profile.d
[?]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[-]: Package contains desktop file if it is a GUI application.
[-]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
Provides are present.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: Useful -debuginfo package or justification otherwise.
[!]: Package is not known to require an ExcludeArch tag.
[x]: Large documentation must go in a -doc subpackage. Large could be size
(~1MB) or number of files.
Note: Documentation size is 10240 bytes in 1 files.
[!]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least one
supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
Note: There are rpmlint messages (see attachment).
[x]: If (and only if) the source package includes the text of the license(s)
in its own file, then that file, containing the text of the license(s)
for the package is included in %doc.
[x]: Package requires other packages for directories it uses.
[x]: Package does not own files or directories owned by other packages.
[x]: All build dependencies are listed in BuildRequires, except for any that
are listed in the exceptions section of Packaging Guidelines.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install' ' DESTDIR=... doesn't
work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package do not use a name that already exist
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as provided
in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
%{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #23 from marcindulak --- GA is FTBFS on ARM bug #964424 . By they way i think that bug should also have Blocks: F-ExcludeArch-arm For the moment i placed that bug in the nwchem.spec file comment. Spec URL: http://marcindulak.fedorapeople.org/packages/nwchem/r05/nwchem.spec SRPM URL: http://marcindulak.fedorapeople.org/packages/nwchem/r05/nwchem-6.3.2-5.fc21.src.rpm -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #22 from Antonio Trande --- "Fedora packagers should make every effort to support all primary architectures." If nwchem cannot be built (or doesn't work) on ARM (http://koji.fedoraproject.org/koji/taskinfo?taskID=6450997), follow these guidelines http://fedoraproject.org/wiki/Packaging:Guidelines#Architecture_Support. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #21 from marcindulak --- koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=6449305 Spec URL: http://marcindulak.fedorapeople.org/packages/nwchem/r04/nwchem.spec SRPM URL: http://marcindulak.fedorapeople.org/packages/nwchem/r04/nwchem-6.3.2-4.fc21.src.rpm -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #20 from Antonio Trande --- Please, document this situation in a specfile comment. Then, I'll start the final review. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #19 from marcindulak --- (In reply to Antonio Trande from comment #18) > (In reply to marcindulak from comment #17) > > This is also visible from all tests suspiciously failed in koji's build.log. > > There are ~1000 and ~4000 source files in nwchem compiled with debug and > > optimization flags, respectively, and the build time 2-3 hours. > > Have you even informed upstream ? i have been involved in some discussions on the nwchem forums, and the focus there is usually to get the code to compile and run at all on different high performance systems. It's a scientific code, and as such has only a "best effort" support. Also one cannot really rely on the QA test set (i don't know if the situation described here improved http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id133/). The full test set includes ~400 cases (there is no concept of unit testing there - these are regular nwchem runs, some VERY heavy), and what i run during the rpmbuild is a small subset of 20. Of course when the nwchem RPM gets into Fedora i will drop a note at the nwchem forum, and mention compilation flags requirement problem. > > > > > Therefore, in my opinion, we have to stick to the default nwchem flags. > > I understand your position. I can just suggest to ask a Bundled Libraries > exception in order to resolve this problem. > http://fedoraproject.org/wiki/Packaging:No_Bundled_Libraries#Exceptions i was not clear enough. nwchem does not distribute GA, it compiles it in the executables. So - it's only a question about dropping %optflags or not. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #18 from Antonio Trande --- (In reply to marcindulak from comment #17) > This is also visible from all tests suspiciously failed in koji's build.log. > There are ~1000 and ~4000 source files in nwchem compiled with debug and > optimization flags, respectively, and the build time 2-3 hours. Have you even informed upstream ? > > Therefore, in my opinion, we have to stick to the default nwchem flags. I understand your position. I can just suggest to ask a Bundled Libraries exception in order to resolve this problem. http://fedoraproject.org/wiki/Packaging:No_Bundled_Libraries#Exceptions -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 marcindulak changed: What|Removed |Added Flags|needinfo?(Marcin.Dulak@gmai | |l.com) | --- Comment #17 from marcindulak --- I have been fighting with nwchem build system for the last couple of days, and at the end managed to replace all (i hope) nwchem compiler flags with %optflags (minus -Werror=format-security - some parts of GA do not compile with that flag on). See http://koji.fedoraproject.org/koji/taskinfo?taskID=6429073 The resulting binaries fail with "texas_init: alloc for texas mapping1 failed 911" for the following example, on Rawhide i686: source /etc/profile.d/nwchem.sh; module load mpi; mpiexec -np 2 `which nwchem_openmpi` nwchem.nw with the following nwchem.nw: geometry noautoz noautosym H 0.0 0.0 1.0 H 0.0 0.0 0.0 end basis spherical * library cc-pvdz end task dft energy This is also visible from all tests suspiciously failed in koji's build.log. There are ~1000 and ~4000 source files in nwchem compiled with debug and optimization flags, respectively, and the build time 2-3 hours. Therefore, in my opinion, we have to stick to the default nwchem flags. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Antonio Trande changed: What|Removed |Added CC||marcin.du...@gmail.com Flags||needinfo?(Marcin.Dulak@gmai ||l.com) --- Comment #16 from Antonio Trande --- Any news ? -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605
--- Comment #15 from Antonio Trande ---
(In reply to marcindulak from comment #13)
> nwchem contains also additional packages (global arrays - i think they
> distribute their own, modified version) and one would have to deal with
> compiler flags also there.
If GA is modified, you should ask an exception about its packaging in nwchem;
otherwise you must use the GA provided by Fedora repositories.
> Moreover, nwchem is a big, complex program, and
> nobody knows how it will react to RPM_OPT_FLAGS,
> and in case of problems we will be asked to go back to the default nwchem
> compiler flags.
> I hope it is a sufficient rationale for letting nwchem to handle compiler
> flags itself.
Try the patch that I uploaded; it's done quickly but it's a good start point
Following there are all changes I've done on your .spec file:
--- nwchem.orig.spec2014-01-15 13:59:41.0 +0100
+++ nwchem.spec2014-01-15 22:38:02.055348143 +0100
@@ -44,6 +44,7 @@
URL:http://www.nwchem-sw.org/
# Nwchem changes naming convention of tarballs very often!
Source0:
http://www.nwchem-sw.org/images/%{upstream_name}-%{major_version}.revision%{minor_version}-src.%{posttag}.tar.gz
+Patch0: nwchem-makefile_flags.patch
%global PKG_TOP
${RPM_BUILD_DIR}/%{name}-%{major_version}.revision%{minor_version}-src.%{posttag}
@@ -123,7 +124,11 @@
%prep
%setup -q -n %{name}-%{major_version}.revision%{minor_version}-src.%{posttag}
+%patch0 -p1
+sed -e 's|@@OPTFLAGS@@|%{optflags}|g' -i src/config/makefile.h
+sed -e 's|@@OPTFLAGS@@|%{optflags}|g' -i src/tools/ga-5-2/armci/configure
+sed -e 's|@@OPTFLAGS@@|%{optflags}|g' -i src/tools/ga-5-2/comex/configure
%build
# base settings
@@ -145,13 +150,17 @@
%endif
echo export HAS_BLAS=yes >> settings.sh
echo export BLASOPT="'%{BLASOPT}'" >> settings.sh
+GA_COPT_FLAGS=$(echo $RPM_OPT_FLAGS | %{__sed} -e
's/-Werror=format-security//')
+echo export GA_COPT="'$GA_COPT_FLAGS'" >> settings.sh
+GA_FOPT_FLAGS=$(echo $RPM_OPT_FLAGS | %{__sed} -e
's/-Werror=format-security//')
+echo export GA_FOPT="'$GA_FOPT_FLAGS'" >> settings.sh
#
# make
echo "# see
https://fedoraproject.org/wiki/Packaging:Guidelines#Compiler_flags"; >>
settings.sh
# double-quotes outside in order to expand RPM_OPT_FLAGS
# RPM_OPT_FLAGS are not used despite the comment
# "can be overridden on the command line" in src/config/makefile.h
-echo export MAKE="%{__make} FOPTIMIZE='${RPM_OPT_FLAGS}'
COPTIMIZE='${RPM_OPT_FLAGS}'" >> settings.sh
+echo export MAKE="%{__make}" >> settings.sh
echo '$MAKE nwchem_config NWCHEM_MODULES="all python" 2>&1 | tee
../make_nwchem_config.log' > make.sh
%if 0%{?make64_to_32}
echo '$MAKE 64_to_32 2>&1 | tee ../make_64_to_32.log' >> make.sh
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[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #14 from Antonio Trande --- Created attachment 850719 --> https://bugzilla.redhat.com/attachment.cgi?id=850719&action=edit Optimization flags patch -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #13 from marcindulak --- (In reply to Antonio Trande from comment #12) > Initial comments: > > - Some 'install' commands are not performed with -p option to preserve > timestamps should be OK now > - I don't see some optimization flag, they are requested by the guidelines i tried exporting FFLAGS, CFLAGS, FOPTIMIZE, COPTIMIZE as mentioned in https://svn.pnl.gov/svn/nwchem/trunk/src/config/makefile.h , but without success (koji: grep "\-O2" build.log - very large file!). It looks like one would have to patch the nwchem Makefiles in order to set different compiler flags. I see that debian http://ftp.de.debian.org/debian/pool/main/n/nwchem/nwchem_6.3+r1-1.debian.tar.gz (e.g. debian/patches/02_makefile_flags.patch) touched the makefile system of nwchem, however nwchem contains also additional packages (global arrays - i think they distribute their own, modified version) and one would have to deal with compiler flags also there. Moreover, nwchem is a big, complex program, and nobody knows how it will react to RPM_OPT_FLAGS, and in case of problems we will be asked to go back to the default nwchem compiler flags. I hope it is a sufficient rationale for letting nwchem to handle compiler flags itself. koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=6405852 Spec URL: http://marcindulak.fedorapeople.org/packages/nwchem/r03/nwchem.spec SRPM URL: http://marcindulak.fedorapeople.org/packages/nwchem/r03/nwchem-6.3.2-3.fc21.src.rpm -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #12 from Antonio Trande --- Initial comments: - Some 'install' commands are not performed with -p option to preserve timestamps - I don't see some optimization flag, they are requested by the guidelines -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 Antonio Trande changed: What|Removed |Added Status|NEW |ASSIGNED Assignee|nob...@fedoraproject.org|anto.tra...@gmail.com Flags||fedora-review? --- Comment #11 from Antonio Trande --- Please, be patience for a little while, this review needs attention. -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #10 from marcindulak --- Nwchem 6.3.2 ready for review koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=6359089 Spec URL: http://marcindulak.fedorapeople.org/packages/nwchem/r02v02/nwchem.spec SRPM URL: http://marcindulak.fedorapeople.org/packages/nwchem/r02v02/nwchem-6.3.2-2.fc21.src.rpm -- You are receiving this mail because: You are on the CC list for the bug. You are always notified about changes to this product and component ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #9 from marcindulak --- The new spec is ready for reviews -- You are receiving this mail because: You are on the CC list for the bug. Unsubscribe from this bug https://bugzilla.redhat.com/token.cgi?t=aXfRSLTaCa&a=cc_unsubscribe ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #8 from marcindulak --- (In reply to Susi Lehtola from comment #7) > By the way, > %ifarch i386 i586 i686 > should read > %ifarch %ix86 i have made that minor change without creating a new release. Also disabled one more nwchem test (h2o-response) that hangs (mpich) or core dumps (serial). I noticed that %ix86 is claimed to become obsolete one day, already at least since 2002 http://www.redhat.com/archives/rpm-list/2002-January/msg00044.html -- You are receiving this mail because: You are on the CC list for the bug. Unsubscribe from this bug https://bugzilla.redhat.com/token.cgi?t=rt461vn7iY&a=cc_unsubscribe ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #6 from marcindulak --- This fixes bug #984605 comment #2 and hopefully conforms to http://fedoraproject.org/wiki/Packaging:MPI#Packaging_of_MPI_software It builds the serial, openmpi and mpich versions. The basis sets, pseudopotentials are in the nwchem-common package instead of nwchem-data. Spec URL: http://marcindulak.fedorapeople.org/packages/nwchem/v02/nwchem.spec SRPM URL: http://marcindulak.fedorapeople.org/packages/nwchem/v02/nwchem-6.3.1-2.fc20.src.rpm -- You are receiving this mail because: You are on the CC list for the bug. Unsubscribe from this bug https://bugzilla.redhat.com/token.cgi?t=z7ccixN0DB&a=cc_unsubscribe ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #7 from Susi Lehtola --- By the way, %ifarch i386 i586 i686 should read %ifarch %ix86 -- You are receiving this mail because: You are on the CC list for the bug. Unsubscribe from this bug https://bugzilla.redhat.com/token.cgi?t=uKSw4Wf5I6&a=cc_unsubscribe ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605 --- Comment #5 from Susi Lehtola --- (In reply to marcindulak from comment #4) > (In reply to Susi Lehtola from comment #3) > > The package MUST conform to the MPI guidelines. Also, you should add an > > mpich2 flavor. > OK - i found this > http://fedoraproject.org/wiki/Packaging:MPI#Packaging_of_MPI_software but > can you suggest me a recent, good style MPI software spec as a template? I > think i will drop el5 - it does not use this new packaging convention. Well, you can look at cp2k or gromacs, for instance. > > You don't need to conditionalize the BuildRoot etc statements for EL5. The > > statements work just fine on newer distros as well. > but fedora-review complains about some of them, so i got suggestion to > include them conditionally for el5 in bug #976886 comment #4 Then this is a bug in fedora-review. Fedora-review is just a simple and dumb tool, which may not be totally in touch with Fedora policies. Having the statements doesn't hurt anything; if you don't have them, new versions of rpm just use default values. -- You are receiving this mail because: You are on the CC list for the bug. Unsubscribe from this bug https://bugzilla.redhat.com/token.cgi?t=tksld6nFxx&a=cc_unsubscribe ___ package-review mailing list package-review@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605
--- Comment #4 from marcindulak ---
(In reply to Susi Lehtola from comment #3)
> The package MUST conform to the MPI guidelines. Also, you should add an
> mpich2 flavor.
OK - i found this
http://fedoraproject.org/wiki/Packaging:MPI#Packaging_of_MPI_software but can
you suggest me a recent, good style MPI software spec as a template? I think i
will drop el5 - it does not use this new packaging convention.
>
> **
>
> # openmpi needs ssh
> BuildRequires:openssh-clients
>
> This doesn't seem right. OpenMPI works just fine without ssh.
i needed that on build.opensuse.org, but confirmed not needed for build
on localhost.
>
> **
>
>
> %if 0%{?el5}
> BuildRequires:blas-devel
> Requires: blas
> %else
> BuildRequires:atlas-devel
> Requires: atlas
> %endif
>
> This is unnecessary. BuildRequires: atlas-devel is available also on EL5.
> Besides, the explicit require is unnecessary and thus banned by guidelines.
OK
>
> **
>
> You don't need to conditionalize the BuildRoot etc statements for EL5. The
> statements work just fine on newer distros as well.
but fedora-review complains about some of them, so i got suggestion to include
them conditionally for el5 in bug #976886 comment #4
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[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605
Susi Lehtola changed:
What|Removed |Added
CC||susi.leht...@iki.fi
Blocks||505154 (FE-SCITECH)
--- Comment #3 from Susi Lehtola ---
The package MUST conform to the MPI guidelines. Also, you should add an mpich2
flavor.
**
# openmpi needs ssh
BuildRequires:openssh-clients
This doesn't seem right. OpenMPI works just fine without ssh.
**
%if 0%{?el5}
BuildRequires:blas-devel
Requires:blas
%else
BuildRequires:atlas-devel
Requires:atlas
%endif
This is unnecessary. BuildRequires: atlas-devel is available also on EL5.
Besides, the explicit require is unnecessary and thus banned by guidelines.
**
You don't need to conditionalize the BuildRoot etc statements for EL5. The
statements work just fine on newer distros as well.
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[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605
--- Comment #2 from marcindulak ---
Yes, we could have %{major_version} 6.3 and just one %{minor_version}, possibly
%{nil}.
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[Bug 984605] Review Request: nwchem - Delivering High-Performance Computational Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=984605
Christopher Meng changed:
What|Removed |Added
CC||cicku...@gmail.com
--- Comment #1 from Christopher Meng ---
Is it possible to directly use 6.3 instead of
%{major_version}.%{minor_version1}?
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