[MacPorts] #39282: Submission: octopus
#39282: Submission: octopus ------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: | Port: octopus ------------------------+-------------------------------- Portfile for Octopus, a time-dependent density-functional theory code, intended for the science category. -- Ticket URL: <https://trac.macports.org/ticket/39282> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by ryandesign@…): Thanks. Some observations: These lines can be removed because they are the defaults: {{{ distfiles octopus-${version}.tar.gz extract.suffix .tar.gz extract.cmd tar extract.pre_args -xzf }}} Setting `FCFLAGS=-O3 CFLAGS=-O3` in `configure.args` can be more simply accomplished by setting `configure.optflags` to `-O3`. The port version is 4.1.0 but the livecheck says the latest version is 4.0.1. Perhaps livechecking http://www.tddft.org/programs/octopus/download/ would be more accurate. Downloading from there would be better too because it would [wiki:howto/AvoidRedirects avoid an HTTP redirect]. The checksums don't match. The universal variant doesn't work: {{{ Error: Cannot install octopus for the arch(s) 'i386 x86_64' because Error: its dependency libxc does not build for the required arch(s) by default Error: and does not have a universal variant. }}} You could disable the universal variant to resolve that. Usually we'd like to add a universal variant if possible, but these ports use gcc4x ports to compile, which makes a universal variant difficult. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:1> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by dstrubbe@…): Sorry about the version confusion. I did mean to put 4.1.0 -- it is not actually released yet, though the tarball is available. I am a developer of this code, and we are planning to release very shortly (days, hopefully). Knowing that it takes a little time to check issues with a new port, I thought I would get the process started even though the release didn't come out yet, so it is ready then. Here is a revised Portfile, with some other enhancements; see what you think. I will confirm here when the release is live and the port can actually be committed. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:2> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by dstrubbe@…): This release is now live. This should fix the livecheck and checksum issues. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:3> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by larryv@…): Replying to [comment:3 dstrubbe@…]:
This release is now live. This should fix the livecheck and checksum issues.
A few more things: - We prefer RMD160 and SHA256 for Portfile checksums. You should leave out SHA1, unless upstream publishes a SHA1 hash. - The default for `use_parallel_build` is already “yes”, so you can leave that out. - The default for `test.cmd` is the value of `build.cmd`, which defaults to “make”, so you can leave that out if you haven’t changed `build.cmd`. - Using `active_variants` procs directly in variant scripts will cause issues when MacPorts processes the Portfile on systems that don’t have the pertinent ports present. See [https://lists.macosforge.org/pipermail /macports-dev/2013-June/023047.html this macports-dev post]. In short, they need to be in a `pre-configure` script. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:4> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by dstrubbe@…): Thanks. I switched to SHA256, updated checksums, fixed master_sites, moved configure.args outside pre-configure (or else the configure.args-append in the variants scripts didn't seem to do anything), removed the defaults you mention, and moved the require_active_variants calls to pre-configure. However, the require_active_variants don't seem to have any effect now; I can't figure out what the problem is. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:5> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by cal@…): Replying to [comment:4 larryv@…]:
- Using `active_variants` procs directly in variant scripts will cause issues when MacPorts processes the Portfile on systems that don’t have the pertinent ports present. See [https://lists.macosforge.org/pipermail /macports-dev/2013-June/023047.html this macports-dev post]. In short, they need to be in a `pre-configure` script.
This only applies to `active_variants 1.0` and has been fixed in `active_variants 1.1`. Please move `require_active_variants` out of the pre-configure phase again. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:6> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by dstrubbe@…): All right, I have moved require_active_variants back again, and it seems to work again. Does the Portfile look good now? -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:7> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Changes (by cal@…): * cc: cal@… (added) Comment: The build fails for me: {{{ ********************************************** *** octopus + utilities will be generated ********************************************** checking for libxc... yes (-I /opt/local/include /opt/local/lib/libxc.a) checking for sgemm in -lsatlas... yes (-lsatlas) checking whether zdotc works... yes checking for cheev in ... yes () checking for gsl-config... /opt/local/bin/gsl-config checking for GSL - version >= 1.9... 1.15.0 checking whether GSL can be linked... yes checking for dfftw_plan_dft_1d... no checking for dfftw_plan_dft_1d in -lfftw3... no checking for dfftw_init_threads... no configure: error: Could not find required FFT library. Command failed: cd "/opt/local/var/macports/build/_opt_dports_science_octopus/octopus/work/octopus-4.1.0" && ./configure --prefix=/opt/local --with-libxc-prefix=/opt/local --with- blas=-lsatlas --disable-gdlib --without-sparskit --enable-newuoa FCCPP="/opt/local/bin/cpp-mp-4.7 -ansi" Exit code: 1 }}} I'm attaching `config.log`. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:8> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by dstrubbe@…): Hm, thanks for checking it out. Did the port correctly make sure you had fftw-3 installed? What version of fftw-3 do you have? This is what my fftw-3 @3.3.3_1+gcc46 gives me; does yours differ? {{{ $ port contents fftw-3 Port fftw-3 contains: /opt/local/bin/fftw-wisdom /opt/local/bin/fftw-wisdom-to-conf /opt/local/include/fftw3.f /opt/local/include/fftw3.f03 /opt/local/include/fftw3.h /opt/local/include/fftw3l.f03 /opt/local/include/fftw3q.f03 /opt/local/lib/libfftw3.3.dylib /opt/local/lib/libfftw3.a /opt/local/lib/libfftw3.dylib /opt/local/lib/libfftw3.la /opt/local/lib/libfftw3_threads.3.dylib /opt/local/lib/libfftw3_threads.a /opt/local/lib/libfftw3_threads.dylib /opt/local/lib/libfftw3_threads.la /opt/local/lib/pkgconfig/fftw3.pc /opt/local/share/info/fftw3.info /opt/local/share/info/fftw3.info-1 /opt/local/share/info/fftw3.info-2 /opt/local/share/man/man1/fftw-wisdom-to-conf.1.gz /opt/local/share/man/man1/fftw-wisdom.1.gz }}} -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:9> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by cal@…): I do have `fftw-3` installed: {{{ :) clemens@cschlepptop:~$ port -v installed fftw-3 The following ports are currently installed: fftw-3 @3.3.3_1 (active) platform='darwin 12' archs='x86_64' }}} The symbols configure checks for don't seem to be present in my `libfftw3.3.dylib`, though: {{{ :) clemens@cschlepptop:~$ nm /opt/local/lib/libfftw3.3.dylib | grep dfftw :( clemens@cschlepptop:~$ }}} Do I need to build `fftw-3` with a specific variant? -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:10> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by cal@…): Answering my own question: Yes, it seems `fftw-3 +gcc47` does have these symbols. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:11> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by cal@…): It also seems to me configure will pick up "automagic" dependencies, if they are present: {{{ configure: WARNING: Could not find NetCDF library. *** Will compile without NetCDF and ETSF I/O support checking for etsf_io... disabled (-I /usr/include ) configure: WARNING: Could not find etsf_io library. *** Will compile without ETSF I/O support checking for BerkeleyGW... no (-I /library -L/library -lBGW_wfn) configure: WARNING: Could not find BerkeleyGW library. *** Will compile without BerkeleyGW support checking for arpack library... no checking for arpack library with -larpack... no configure: WARNING: Could not find ARPACK library. *** Will compile without ARPACK support configure: WARNING: Could not find Libfm library. *** Will compile without Libfm support configure: WARNING: Could not find PFFT library. *** Will compile without PFFT support }}} To keep the build reproducible and to avoid linking against a port without specifying a dependency you should explicitly disable those by passing arguments to configure. If you want to support these libraries, add variants or add a dependency. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:12> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: | Keywords: Port: octopus | -------------------------+-------------------------------- Comment (by dstrubbe@…): Ok, fftw-3 needs a Fortran variant, so I added a check. And I explicitly disabled these other libraries. Many are not available as ports anyway. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:13> MacPorts <http://www.macports.org/> Ports system for OS X
#39282: Submission: octopus -------------------------+-------------------------------- Reporter: dstrubbe@… | Owner: macports-tickets@… Type: submission | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Resolution: fixed | Keywords: Port: octopus | -------------------------+-------------------------------- Changes (by cal@…): * status: new => closed * resolution: => fixed Comment: LGTM, commited in r107233. Thank you for your work. -- Ticket URL: <https://trac.macports.org/ticket/39282#comment:14> MacPorts <http://www.macports.org/> Ports system for OS X
participants (1)
-
MacPorts