Spec URL: http://rathann.fedorapeople.org/review/elpa/elpa.spec SRPM URL: http://rathann.fedorapeople.org/review/elpa/elpa-2013.11-1.008.fc20.src.rpm Description: ELPA is a Fortran-based high-performance computational library for the (massively) parallel solution of symmetric or Hermitian, standard or generalized eigenvalue problems. This is the kind of eigenvalue problem which is frequently encountered in Electronic Structure Theory (solution of Schrödinger's Equation or variants thereof), but also in many other fields. Typically, the solution effort scales as O(size^3), where "size" is a measure of the system size, for example the dimension of the associated matrices or the number of required eigenvalue/eigenvector pairs (less than or equal to the matrix dimension). Thus, an algebraically exact solution of the eigenproblem may quickly become the bottleneck in a practical application. Fedora Account System Username: rathann
I've just been doing it; never mind. Would you accept a patch for EPEL6? (cp2k 2.5 builds on EPEL6 with devtoolset-2, and I was going to put it in copr when I'd rebuilt against elpa.) I had to avoid patching configure since it needs more recent autotools than in EPEL6, and I'd have to check that recipe for the Fedora releases. I can't find any packaging rules about library names, but wouldn't it be better to call it libelpa? If nothing else it helps things like rpmorphan. It would probably be useful to package versions with other optimizations, like sandybridge in our case, but I wasn't sure how best to do it and couldn't find any examples. I wonder if there should be a policy on that.
Issues: - A comment why %{?_smp_mflags} is disabled would be nice - Comment how to obtain source tarball - Unowned directory issues: * No package seems to own %{_libdir}/gfortran (possibly gfortran should do so?) * Same goes with %{_libdir}/*mpi*/pkgconfig - rpmlint * undefined-non-weak-symbol : these should be fixable my linking against the mpi / gomp libraries * unused-direct-shlib-dependency : could try -Wl,--as-needed Note: - Spec in SRPM differs Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= - All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines. Note: These BR are not needed: sed See: http://fedoraproject.org/wiki/Packaging/Guidelines#Exceptions_2 ===== 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. [x]: Development (unversioned) .so files in -devel subpackage, if present. 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. [x]: License file installed when any subpackage combination is installed. [x]: Package requires other packages for directories it uses. Note: No known owner of /usr/lib64/gfortran, /usr/lib64/gfortran/modules, /usr/lib64/openmpi/lib/pkgconfig, /usr/lib64/gfortran/modules/mpich, /usr/lib64/mpich/lib/pkgconfig, /usr/lib64/gfortran/modules/openmpi => Not a blocker since there are no packages which provide these directories [x]: Package must own all directories that it creates. Note: Directories without known owners: /usr/lib64/gfortran, /usr/lib64/openmpi/lib, /usr/lib64/gfortran/modules, /usr/lib64/mpich, /usr/lib64/mpich/lib, /usr/lib64/openmpi/lib/pkgconfig, /usr/lib64/gfortran/modules/mpich, /usr/lib64/mpich/lib/pkgconfig, /usr/lib64/openmpi, /usr/lib64/gfortran/modules/openmpi => Not a blocker since there are no packages which provide these directories [x]: %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. [x]: 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. [x]: Package is not known to require an ExcludeArch tag. [-]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 61440 bytes in 4 files. [x]: 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 does not own files or directories owned by other packages. [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 must not store files under /srv, /opt or /usr/local ===== SHOULD items ===== Generic: [!]: Uses parallel make %{?_smp_mflags} macro. [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [x]: Final provides and requires are sane (see attachments). [x]: Fully versioned dependency in subpackages if applicable. [?]: Package functions as described. [?]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Patches link to upstream bugs/comments/lists or are otherwise justified. [x]: Scriptlets must be sane, if used. [!]: SourceX tarball generation or download is documented. Note: Package contains tarball without URL, check comments [-]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [?]: Package should compile and build into binary rpms on all supported architectures. [x]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: Dist tag is present (not strictly required in GL). [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: The placement of pkgconfig(.pc) files are correct. [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== EXTRA items ===== Generic: [!]: Spec file according to URL is the same as in SRPM. Note: Spec file as given by url is not the same as in SRPM (see attached diff). See: (this test has no URL) [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched. [x]: Package should not use obsolete m4 macros Rpmlint ------- Checking: elpa-common-2013.11-1.008.fc21.noarch.rpm elpa-mpich-2013.11-1.008.fc21.x86_64.rpm elpa-mpich-devel-2013.11-1.008.fc21.x86_64.rpm elpa-openmpi-2013.11-1.008.fc21.x86_64.rpm elpa-openmpi-devel-2013.11-1.008.fc21.x86_64.rpm elpa-2013.11-1.008.fc21.src.rpm elpa-mpich.x86_64: W: no-documentation elpa-mpich-devel.x86_64: W: only-non-binary-in-usr-lib elpa-mpich-devel.x86_64: W: no-documentation elpa-openmpi.x86_64: W: no-documentation elpa-openmpi-devel.x86_64: W: only-non-binary-in-usr-lib elpa-openmpi-devel.x86_64: W: no-documentation elpa.src: W: spelling-error %description -l en_US eigenvector -> convector elpa.src: W: spelling-error %description -l en_US eigenproblem -> problematic elpa.src: W: invalid-url Source0: ELPA_2013.11.tar.xz 6 packages and 0 specfiles checked; 0 errors, 9 warnings. Rpmlint (installed packages) ---------------------------- # rpmlint elpa-mpich-devel elpa-openmpi-devel elpa-common elpa-openmpi elpa-mpich elpa-mpich-devel.x86_64: W: only-non-binary-in-usr-lib elpa-mpich-devel.x86_64: W: no-documentation elpa-openmpi-devel.x86_64: W: only-non-binary-in-usr-lib elpa-openmpi-devel.x86_64: W: no-documentation elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_reduce_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_isend_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_comm_split_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_abort_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_test_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_comm_rank_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_sendrecv_replace_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_wait_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_wtime_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_waitall_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_sendrecv_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_irecv_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_barrier_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_alltoallv_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_recv_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_send_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_allreduce_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_comm_size_ elpa-openmpi.x86_64: W: undefined-non-weak-symbol /usr/lib64/openmpi/lib/libelpa.so.0.0.0 mpi_bcast_ elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 libscalapack.so.2 elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 libmpiblacs.so.2 elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 /lib64/libstdc++.so.6 elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 /lib64/libgcc_s.so.1 elpa-openmpi.x86_64: W: no-documentation elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_reduce_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 GOMP_parallel elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_isend_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_comm_split_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_abort_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_test_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_comm_rank_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_sendrecv_replace_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_wait_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_wtime_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 omp_get_thread_num_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_waitall_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_sendrecv_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_irecv_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_barrier_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 omp_get_num_threads_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 omp_get_num_threads elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_alltoallv_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_recv_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_send_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_allreduce_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 omp_get_max_threads_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 GOMP_barrier elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_comm_size_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 omp_get_thread_num elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 mpi_bcast_ elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 libscalapack.so.2 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 libmpiblacs.so.2 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /lib64/libstdc++.so.6 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /lib64/libgcc_s.so.1 elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_reduce_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_isend_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_comm_split_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_abort_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_test_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_comm_rank_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_sendrecv_replace_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_wait_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_wtime_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_waitall_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_sendrecv_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_irecv_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_barrier_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_alltoallv_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_recv_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_send_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_allreduce_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_comm_size_ elpa-mpich.x86_64: W: undefined-non-weak-symbol /usr/lib64/mpich/lib/libelpa.so.0.0.0 mpi_bcast_ elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 libscalapack.so.2 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 libmpiblacs.so.2 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /lib64/libstdc++.so.6 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /lib64/libgcc_s.so.1 elpa-mpich.x86_64: W: no-documentation 5 packages and 0 specfiles checked; 0 errors, 82 warnings. # echo 'rpmlint-done:' Diff spec file in url and in SRPM --------------------------------- --- /home/sandro/.Data/Desktop/1112864-elpa/srpm/elpa.spec 2014-06-25 15:52:47.784991580 +0200 +++ /home/sandro/.Data/Desktop/1112864-elpa/srpm-unpacked/elpa.spec 2014-06-24 10:56:21.000000000 +0200 @@ -195,5 +195,4 @@ rm %{buildroot}%{_bindir}/test* -%if 0 %check %{_mpich_load} @@ -212,5 +211,4 @@ popd %{_openmpi_unload} -%endif %post mpich -p /sbin/ldconfig Requires -------- elpa-mpich-devel (rpmlib, GLIBC filtered): elpa-mpich(x86-64) libelpa.so.0()(64bit) libelpa_mt.so.0()(64bit) elpa-openmpi-devel (rpmlib, GLIBC filtered): elpa-openmpi(x86-64) libelpa.so.0()(64bit) elpa-common (rpmlib, GLIBC filtered): elpa-openmpi (rpmlib, GLIBC filtered): /sbin/ldconfig blacs-openmpi elpa-common libblas.so.3()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) liblapack.so.3()(64bit) libm.so.6()(64bit) libmpiblacs.so.2()(64bit) libscalapack.so.2()(64bit) libstdc++.so.6()(64bit) rtld(GNU_HASH) scalapack-openmpi elpa-mpich (rpmlib, GLIBC filtered): /sbin/ldconfig blacs-mpich elpa-common libblas.so.3()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) liblapack.so.3()(64bit) libm.so.6()(64bit) libmpiblacs.so.2()(64bit) libscalapack.so.2()(64bit) libstdc++.so.6()(64bit) rtld(GNU_HASH) scalapack-mpich Provides -------- elpa-mpich-devel: elpa-mpich-devel elpa-mpich-devel(x86-64) elpa-openmpi-devel: elpa-openmpi-devel elpa-openmpi-devel(x86-64) elpa-common: elpa-common elpa-openmpi: elpa-openmpi elpa-openmpi(x86-64) libelpa.so.0()(64bit) elpa-mpich: elpa-mpich elpa-mpich(x86-64) libelpa.so.0()(64bit) libelpa_mt.so.0()(64bit) Generated by fedora-review 0.5.1 (bb9bf27) last change: 2013-12-13 Command line :/usr/bin/fedora-review -b 1112864 Buildroot used: fedora-rawhide-x86_64 Active plugins: Generic, Shell-api, C/C++ Disabled plugins: Java, Python, fonts, SugarActivity, Ocaml, Perl, Haskell, R, PHP, Ruby Disabled flags: EXARCH, EPEL5, BATCH, DISTTAG
(In reply to Dave Love from comment #1) > I've just been doing it; never mind. > > Would you accept a patch for EPEL6? Of course. I'll most likely keep it in that branch only, though. > I can't find any packaging rules about library names, but wouldn't it be > better to call it libelpa? If nothing else it helps things like rpmorphan. Upstream calls it ELPA. The naming (https://fedoraproject.org/wiki/Packaging:NamingGuidelines) guidelines don't mandate any lib* prefix for libraries and suggest using upstream naming. > It would probably be useful to package versions with other optimizations, > like sandybridge in our case, but I wasn't sure how best to do it and > couldn't find any examples. I wonder if there should be a policy on that. atlas and qtwebkit do something like that, for example, but only for i686 with and without SSE2 support. Unfortunately, hwcap support is completely undocumented (see my 6 year old bug: https://sourceware.org/bugzilla/show_bug.cgi?id=7100) and no hwcaps are defined on x86_64 (check /usr/include/bits/hwcap.h on your system).
(In reply to Sandro Mani from comment #2) > - Unowned directory issues: > * No package seems to own %{_libdir}/gfortran (possibly gfortran should do > so?) In case it's not clear, the guidelines say the devel package needs Requires: gcc-gfortran%{_isa} > * Same goes with %{_libdir}/*mpi*/pkgconfig It looks like an openmpi packaging bug, at least in EPEL6. Its environment module file references the directory, but the package doesn't create it. The mpich2 module file doesn't add to PKG_CONFIG_PATH. This looks like something which should be added to the MPI packaging guidelines. I'd assumed the pc files should have MPI-specific names in the usual directory, put having them in the MPI tree seems sensible.
I've filed [1] about the %{_libdir}/gfortran issue. In the meantime, yes please require gcc-gfortran as the guidelines state. [1] https://bugzilla.redhat.com/show_bug.cgi?id=1113564
(In reply to Sandro Mani from comment #2) > Issues: > - A comment why %{?_smp_mflags} is disabled would be nice > - Comment how to obtain source tarball Fixed. After talking to upstream again, I found the right homepage URL and links to source tarballs there. > - Unowned directory issues: > * No package seems to own %{_libdir}/gfortran (possibly gfortran should do > so?) Fixed by adding the missing Requires on gcc-gfortran, as Dave pointed out. > * Same goes with %{_libdir}/*mpi*/pkgconfig > - rpmlint > * undefined-non-weak-symbol : these should be fixable my linking against > the mpi / gomp libraries I managed to fix that, but I'm still getting undefined symbols due to a bug in scalapack package. Bug 1113567 filed. > * unused-direct-shlib-dependency : could try -Wl,--as-needed It fails at linking when I add that. Also, these come from linking with mpif90 (which is as it turns out required to avoid the undefined mpi symbols). I'll keep trying to fix that. > Note: > - Spec in SRPM differs I'll keep the %if 0 there to allow disabling tests for quick local builds. New spec and srpm: http://rathann.fedorapeople.org/review/elpa/elpa.spec http://rathann.fedorapeople.org/review/elpa/elpa-2013.11-2.008.fc20.src.rpm * Thu Jun 26 2014 Dominik Mierzejewski <rpm> 2013.11-2.008 - remove executable stack from installed libraries - fix undefined non-weak mpi symbols - reorder build section and drop some redundant parts - add missing gfortran Requires for -devel subpackages - use correct URL and provide link to source tarball
> > * Same goes with %{_libdir}/*mpi*/pkgconfig > > It looks like an openmpi packaging bug, at least in EPEL6. Its environment > module file references the directory, but the package doesn't create it. Sorry, ignore that. The module file I had was actually from the fedora-19 package. In RHEL, and later Fedora by the looks of it, pkg-config won't normally find the pc files in the MPI tree.
> Sorry, ignore that. The module file I had was actually from the fedora-19 package. In RHEL, and later Fedora by the looks of it, pkg-config won't normally find the pc files in the MPI tree. In my opinion the openmpi module file should set PKG_CONFIG_PATH to point to the corresponding directory. According to the pkg-config manpage, the default directory will always be searched after PKG_CONFIG_PATH. So it would make perfect sense to override it. Note that also other packages install .pc files in $MPI_LIB/pkg-config.
Bugs filed: openmpi: https://bugzilla.redhat.com/show_bug.cgi?id=1113626 mpich: https://bugzilla.redhat.com/show_bug.cgi?id=1113627
(In reply to Dominik 'Rathann' Mierzejewski from comment #3) > > Would you accept a patch for EPEL6? > > Of course. I'll most likely keep it in that branch only, though. I'll attach the patch I've built with, though it's messy. > > It would probably be useful to package versions with other optimizations, > > like sandybridge in our case, but I wasn't sure how best to do it and > > couldn't find any examples. I wonder if there should be a policy on that. > > atlas and qtwebkit do something like that, for example, but only for i686 > with and without SSE2 support. I hadn't realized atlas was doing that now -- I use openblas when possible. Actually atlas has x86_64 sse2/sse3 versions. I'll look at doing something similar with ELPA unless there's a good reason not to. > Unfortunately, hwcap support is completely > undocumented (see my 6 year old bug: > https://sourceware.org/bugzilla/show_bug.cgi?id=7100) and no hwcaps are > defined on x86_64 (check /usr/include/bits/hwcap.h on your system). Yes, I'd ruled it out long ago, even though it seems to be just what's needed on a typical heterogeneous HPC system. Linux fails to do several things right that would really help HPC...
Created attachment 912845 [details] port to EPEL6
Hmpf, didn't notice that my comment wasn't submitted due to mid-air collission... Anyway, the comment was: elpa-openmpi.x86_64: W: executable-stack /usr/lib64/openmpi/lib/libelpa.so.0.0.0 Rest is good!
The execstack call has a typo -- "mpich" should be "$mpi". Shouldn't it link against openblas/atlas rather than reference blas?
(In reply to Dave Love from comment #11) > Created attachment 912845 [details] > port to EPEL6 Thanks a lot, but I don't think it's worth it to maintain the same spec file across all branches at all cost. I think it'd be easier to drop all non-EL6 parts from the spec alltogether for the EL6 branch. Could you post a diff doing that? Also, please feel encouraged to apply for co-maintainership after this package is approved.
(In reply to Sandro Mani from comment #12) > Hmpf, didn't notice that my comment wasn't submitted due to mid-air > collission... Anyway, the comment was: > > > elpa-openmpi.x86_64: W: executable-stack > /usr/lib64/openmpi/lib/libelpa.so.0.0.0 Fixed. (In reply to Dave Love from comment #13) > The execstack call has a typo -- "mpich" should be "$mpi". > > Shouldn't it link against openblas/atlas rather than reference blas? It is build against atlas now. openblas doesn't support ARM yet. Do you think it's worth it to build against openblas on x86/x86_64 and atlas on ARM? New spec and srpm: http://rathann.fedorapeople.org/review/elpa/elpa.spec http://rathann.fedorapeople.org/review/elpa/elpa-2013.11-3.008.fc20.src.rpm * Sun Jun 29 2014 Dominik Mierzejewski <rpm> 2013.11-3.008 - fix typo in execstack -c call - link against atlas
The reason for # %{?_smp_mflags} should be documented with a comment. But this is not a blocker. Rest is fine, package approved! Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed ===== MUST items ===== C/C++: [ ]: Package does not contain kernel modules. [ ]: Package contains no static executables. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs. [x]: Development (unversioned) .so files in -devel subpackage, if present. 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. [x]: License file installed when any subpackage combination is installed. [x]: Package requires other packages for directories it uses. Note: No known owner of /usr/lib64/gfortran, /usr/lib64/gfortran/modules, /usr/lib64/openmpi/lib/pkgconfig, /usr/lib64/gfortran/modules/mpich, /usr/lib64/mpich/lib/pkgconfig, /usr/lib64/gfortran/modules/openmpi => These directories should be owned by gcc-gfortran resp openmpi/mpich, which are listed as Requires [x]: Package must own all directories that it creates. Note: Directories without known owners: /usr/lib64/gfortran, /usr/lib64/openmpi/lib, /usr/lib64/gfortran/modules, /usr/lib64/mpich, /usr/lib64/mpich/lib, /usr/lib64/openmpi/lib/pkgconfig, /usr/lib64/gfortran/modules/mpich, /usr/lib64/mpich/lib/pkgconfig, /usr/lib64/openmpi, /usr/lib64/gfortran/modules/openmpi => These directories should be owned by gcc-gfortran resp openmpi/mpich, which are listed as Requires [x]: %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. [x]: 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. [x]: Package is not known to require an ExcludeArch tag. [-]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 61440 bytes in 4 files. [x]: 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 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 must not store files under /srv, /opt or /usr/local ===== SHOULD items ===== Generic: [!]: Uses parallel make %{?_smp_mflags} macro. [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [x]: Final provides and requires are sane (see attachments). [x]: Fully versioned dependency in subpackages if applicable. [?]: Package functions as described. [?]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Patches link to upstream bugs/comments/lists or are otherwise justified. [x]: Scriptlets must be sane, if used. [x]: SourceX tarball generation or download is documented. [-]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [?]: Package should compile and build into binary rpms on all supported architectures. [x]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: Dist tag is present (not strictly required in GL). [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: The placement of pkgconfig(.pc) files are correct. [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== EXTRA items ===== Generic: [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched. [x]: Package should not use obsolete m4 macros [x]: Spec file according to URL is the same as in SRPM. Rpmlint ------- Checking: elpa-common-2013.11-3.008.fc21.noarch.rpm elpa-mpich-2013.11-3.008.fc21.x86_64.rpm elpa-mpich-devel-2013.11-3.008.fc21.x86_64.rpm elpa-openmpi-2013.11-3.008.fc21.x86_64.rpm elpa-openmpi-devel-2013.11-3.008.fc21.x86_64.rpm elpa-2013.11-3.008.fc21.src.rpm elpa-mpich.x86_64: W: no-documentation elpa-mpich-devel.x86_64: W: only-non-binary-in-usr-lib elpa-mpich-devel.x86_64: W: no-documentation elpa-openmpi.x86_64: W: no-documentation elpa-openmpi-devel.x86_64: W: only-non-binary-in-usr-lib elpa-openmpi-devel.x86_64: W: no-documentation elpa.src: W: spelling-error %description -l en_US eigenvector -> convector elpa.src: W: spelling-error %description -l en_US eigenproblem -> problematic elpa.src: W: invalid-url Source0: ELPA_2013.11.008_20140321.tar.gz 6 packages and 0 specfiles checked; 0 errors, 9 warnings. Rpmlint (installed packages) ---------------------------- # rpmlint elpa-mpich-devel elpa-openmpi-devel elpa-common elpa-openmpi elpa-mpich elpa-mpich-devel.x86_64: W: only-non-binary-in-usr-lib elpa-mpich-devel.x86_64: W: no-documentation elpa-openmpi-devel.x86_64: W: only-non-binary-in-usr-lib elpa-openmpi-devel.x86_64: W: no-documentation elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 /usr/lib64/openmpi/lib/libscalapack.so.2 elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 /usr/lib64/openmpi/lib/libmpiblacs.so.2 elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 /usr/lib64/openmpi/lib/libmpi.so.1 elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 /lib64/libquadmath.so.0 elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 /lib64/libpthread.so.0 elpa-openmpi.x86_64: W: unused-direct-shlib-dependency /usr/lib64/openmpi/lib/libelpa.so.0.0.0 /lib64/libgcc_s.so.1 elpa-openmpi.x86_64: W: no-documentation elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /usr/lib64/mpich/lib/libscalapack.so.2 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /usr/lib64/mpich/lib/libmpiblacs.so.2 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /usr/lib64/mpich/lib/libmpichf90.so.12 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /usr/lib64/mpich/lib/libopa.so.1 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /usr/lib64/mpich/lib/libmpl.so.1 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /lib64/librt.so.1 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /lib64/libquadmath.so.0 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /lib64/libpthread.so.0 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa_mt.so.0.0.0 /lib64/libgcc_s.so.1 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /usr/lib64/mpich/lib/libscalapack.so.2 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /usr/lib64/mpich/lib/libmpiblacs.so.2 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /usr/lib64/mpich/lib/libmpichf90.so.12 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /usr/lib64/mpich/lib/libopa.so.1 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /usr/lib64/mpich/lib/libmpl.so.1 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /lib64/librt.so.1 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /lib64/libpthread.so.0 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /lib64/libquadmath.so.0 elpa-mpich.x86_64: W: unused-direct-shlib-dependency /usr/lib64/mpich/lib/libelpa.so.0.0.0 /lib64/libgcc_s.so.1 elpa-mpich.x86_64: W: no-documentation 5 packages and 0 specfiles checked; 0 errors, 30 warnings. # echo 'rpmlint-done:' Requires -------- elpa-mpich-devel (rpmlib, GLIBC filtered): elpa-mpich(x86-64) gcc-gfortran(x86-64) libelpa.so.0()(64bit) libelpa_mt.so.0()(64bit) elpa-openmpi-devel (rpmlib, GLIBC filtered): elpa-openmpi(x86-64) gcc-gfortran(x86-64) libelpa.so.0()(64bit) elpa-common (rpmlib, GLIBC filtered): elpa-openmpi (rpmlib, GLIBC filtered): /sbin/ldconfig blacs-openmpi elpa-common libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgfortran.so.3()(64bit) libgfortran.so.3(GFORTRAN_1.0)(64bit) libgfortran.so.3(GFORTRAN_1.4)(64bit) libm.so.6()(64bit) libmpi.so.1()(64bit) libmpi_mpifh.so.2()(64bit) libmpi_usempi.so.1()(64bit) libmpiblacs.so.2()(64bit) libpthread.so.0()(64bit) libquadmath.so.0()(64bit) libsatlas.so.3()(64bit) libscalapack.so.2()(64bit) rtld(GNU_HASH) scalapack-openmpi elpa-mpich (rpmlib, GLIBC filtered): /sbin/ldconfig blacs-mpich elpa-common libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgfortran.so.3()(64bit) libgfortran.so.3(GFORTRAN_1.0)(64bit) libgfortran.so.3(GFORTRAN_1.4)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libmpiblacs.so.2()(64bit) libmpich.so.12()(64bit) libmpichf90.so.12()(64bit) libmpl.so.1()(64bit) libopa.so.1()(64bit) libpthread.so.0()(64bit) libquadmath.so.0()(64bit) librt.so.1()(64bit) libsatlas.so.3()(64bit) libscalapack.so.2()(64bit) rtld(GNU_HASH) scalapack-mpich Provides -------- elpa-mpich-devel: elpa-mpich-devel elpa-mpich-devel(x86-64) elpa-openmpi-devel: elpa-openmpi-devel elpa-openmpi-devel(x86-64) elpa-common: elpa-common elpa-openmpi: elpa-openmpi elpa-openmpi(x86-64) libelpa.so.0()(64bit) elpa-mpich: elpa-mpich elpa-mpich(x86-64) libelpa.so.0()(64bit) libelpa_mt.so.0()(64bit) Generated by fedora-review 0.5.1 (bb9bf27) last change: 2013-12-13 Command line :/usr/bin/fedora-review -b 1112864 Buildroot used: fedora-rawhide-x86_64 Active plugins: Generic, Shell-api, C/C++ Disabled plugins: Java, Python, fonts, SugarActivity, Ocaml, Perl, Haskell, R, PHP, Ruby Disabled flags: EXARCH, EPEL5, BATCH, DISTTAG
New Package SCM Request ======================= Package Name: elpa Short Description: High-performance library for parallel solution of eigenvalue problems Upstream URL: http://elpa.rzg.mpg.de/ Owners: rathann Branches: f19 f20 epel7 el6 InitialCC:
Git done (by process-git-requests).
(In reply to Dominik 'Rathann' Mierzejewski from comment #15) > It is build against atlas now. openblas doesn't support ARM yet. Do you > think it's worth it to build against openblas on x86/x86_64 and atlas on ARM? I don't know what difference it makes in this case, but I'd expect openblas to be maybe twice as fast on sandybridge for DGEMM-based things, at least with the packaged versions. However, when I tried to compare atlas recently, I got strange, non-reproducible results that I haven't tried to understand. If the tests in the ELPA source make a reasonable benchmark, I could maybe try, but I think they didn't run for long. cp2k built with openblas, fftw, and openmpi actually seemed to out-perform a version built with all-intel on a similar cluster on the one case I had a report for, but I haven't tried very serious comparisons, and I've just discovered that the Fedora fftw isn't avx enabled. I'd forgotten to file an issue suggesting it should use openblas.
Bug 1115220 filed for EPEL7 branch blocker. I'll work on building parallel-installable optimized versions, too. As for building against openblas, this would either have to be a distro-wide switch or we should mandate (via Guidelines change) that all alternative blas/lapack implementation provide a drop-in replacement ABI-compatible libraries for libblas.so.* and liblapack.so.*. The latter would have my +1 in a FPC vote.
elpa-2013.11-3.008.fc19 has been submitted as an update for Fedora 19. https://admin.fedoraproject.org/updates/elpa-2013.11-3.008.fc19
elpa-2013.11-3.008.fc20 has been submitted as an update for Fedora 20. https://admin.fedoraproject.org/updates/elpa-2013.11-3.008.fc20
elpa-2013.11-3.008.fc20 has been pushed to the Fedora 20 testing repository.
elpa-2013.11-3.008.fc19 has been pushed to the Fedora 19 stable repository.
elpa-2013.11-3.008.fc20 has been pushed to the Fedora 20 stable repository.