<removed a bunch of warnings>
ERROR: Failed to process easyconfig
/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2018b-OpenBLAS-0.3.1.eb:
Failed to determine minimal toolchain for dep OpenBLAS 0.3.1-GCC-7.3.0-2.30
and a bunch of warnings (full log below).
eb -S OpenBLAS-0.3.1-GCC-7.3.0-2.30
gives
CFGS1=/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs/o/OpenBLAS
* $CFGS1/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb
and
eb OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb -D
== temporary log file in case of crash /tmp/eb-VAv5nH/easybuild-9UafJT.log
Dry run: printing build status of easyconfigs and dependencies
CFGS=/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs
* [x] $CFGS/m/M4/M4-1.4.18.eb (module: M4/1.4.18)
* [x] $CFGS/z/zlib/zlib-1.2.11.eb (module: zlib/1.2.11)
* [x] $CFGS/h/help2man/help2man-1.47.4.eb (module: help2man/1.47.4)
* [x] $CFGS/m/M4/M4-1.4.17.eb (module: M4/1.4.17)
* [x] $CFGS/b/Bison/Bison-3.0.4.eb (module: Bison/3.0.4)
* [x] $CFGS/f/flex/flex-2.6.4.eb (module: flex/2.6.4)
* [x] $CFGS/b/binutils/binutils-2.30.eb (module: binutils/2.30)
* [x] $CFGS/g/GCCcore/GCCcore-7.3.0.eb (module: GCCcore/7.3.0)
* [x] $CFGS/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb (module:
zlib/1.2.11-GCCcore-7.3.0)
* [x] $CFGS/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb (module:
help2man/1.47.4-GCCcore-7.3.0)
* [x] $CFGS/m/M4/M4-1.4.18-GCCcore-7.3.0.eb (module:
M4/1.4.18-GCCcore-7.3.0)
* [x] $CFGS/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb (module:
Bison/3.0.4-GCCcore-7.3.0)
* [x] $CFGS/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb (module:
Bison/3.0.5-GCCcore-7.3.0)
* [x] $CFGS/f/flex/flex-2.6.4-GCCcore-7.3.0.eb (module:
flex/2.6.4-GCCcore-7.3.0)
* [x] $CFGS/b/binutils/binutils-2.30-GCCcore-7.3.0.eb (module:
binutils/2.30-GCCcore-7.3.0)
* [x] $CFGS/g/GCC/GCC-7.3.0-2.30.eb (module: GCC/7.3.0-2.30)
* [x] $CFGS/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb (module:
OpenBLAS/0.3.1-GCC-7.3.0-2.30)
== Temporary log file(s) /tmp/eb-VAv5nH/easybuild-9UafJT.log* have been
removed.
== Temporary directory /tmp/eb-VAv5nH has been removed.
== temporary log file in case of crash /tmp/eb-ZCIA8v/easybuild-JS80fY.log
WARNING: Use of 3 unknown easyconfig parameters detected in
gompi-2018b.eb: binutilsver, gccver, tcver
If these are just local variables please rename them to start with
'local_', or try using --fix-deprecated-easyconfigs to do this
automatically.
For more information, see
https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html
.
WARNING: Deprecated functionality, will no longer work in v5.0: Use of
'dummy' toolchain is deprecated, use 'system' toolchain instead; see
http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html
for more information
WARNING: Use of 3 unknown easyconfig parameters detected in
gompi-2018b.eb: binutilsver, gccver, tcver
If these are just local variables please rename them to start with
'local_', or try using --fix-deprecated-easyconfigs to do this
automatically.
For more information, see
https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html
.
WARNING: Use of 2 unknown easyconfig parameters detected in
GCC-4.9.3-binutils-2.25.eb: binutilsver, mpfr_version
If these are just local variables please rename them to start with
'local_', or try using --fix-deprecated-easyconfigs to do this
automatically.
For more information, see
https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html
.
WARNING: Deprecated functionality, will no longer work in v5.0: Use of
'dummy' toolchain is deprecated, use 'system' toolchain instead; see
http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html
for more information
WARNING: Use of 2 unknown easyconfig parameters detected in
GCC-4.9.3-binutils-2.25.eb: binutilsver, mpfr_version
If these are just local variables please rename them to start with
'local_', or try using --fix-deprecated-easyconfigs to do this
automatically.
For more information, see
https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html
.
WARNING: Use of 2 unknown easyconfig parameters detected in
GNU-4.9.3-2.25.eb: binutilsver, gccver
If these are just local variables please rename them to start with
'local_', or try using --fix-deprecated-easyconfigs to do this
automatically.
For more information, see
https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html
.
WARNING: Use of 3 unknown easyconfig parameters detected in
OpenMPI-1.8.8-GNU-4.9.3-2.25.eb: binfile, libfile, libs
If these are just local variables please rename them to start with
'local_', or try using --fix-deprecated-easyconfigs to do this
automatically.
For more information, see
https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html
.
WARNING: Use of 2 unknown easyconfig parameters detected in
GNU-4.9.3-2.25.eb: binutilsver, gccver
If these are just local variables please rename them to start with
'local_', or try using --fix-deprecated-easyconfigs to do this
automatically.
For more information, see
https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html
.
ERROR: Failed to process easyconfig
/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2018b-OpenBLAS-0.3.1.eb:
Failed to determine minimal toolchain for dep OpenBLAS 0.3.1-GCC-7.3.0-2.30
On Mon, Nov 18, 2019 at 4:28 PM Kenneth Hoste <[email protected]
<mailto:[email protected]>> wrote:
On 18/11/2019 21:50, Niek de Klein wrote:
> Hi Kenneth,
>
> I spoke too soon, some of my installations work but not all. When
I try
> to isntall Autoconf-2.69-foss-2018.eb I get
>
> ERROR: Failed to process easyconfig
>
/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2018b.eb:
> Failed to determine minimal toolchain for dep M4 1.4.17
>
> with eb --search I get:
>
> eb --search M4-1.4.17-foss-2018b
> *
>
/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2018b.eb
>
> eb --search ^foss-2018b.eb
> *
>
/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs/f/foss/foss-2018b.eb
>
> So it can find both the M4-1.4.17-foss-2018b.eb file and the
> foss-2018.eb file.
Can you try "eb M4-1.4.17-foss-2018b.eb -D"?
>
> Kind regards,
> Niek
>
>
>
>
>
> On Mon, Nov 18, 2019 at 3:21 PM Niek de Klein
<[email protected] <mailto:[email protected]>
> <mailto:[email protected] <mailto:[email protected]>>> wrote:
>
> Hi Kenneth,
>
> Thanks for your help!
>
> 1. is solved now with your suggestion of
> EASYBUILD_DISABLE_ENFORCE_CHECKSUMS=1
>
> Now that the bootstrap.py ran correctly it can also find the
> easybuild files in the location that I have configured, so this
> solves 1 and 2 as well.
>
> Thanks,
> Niek
>
> On Mon, Nov 18, 2019 at 3:01 PM Kenneth Hoste
> <[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
>
> Dear Niek,
>
> Sorry that you're hitting these issues, let's try and get
them
> sorted...
>
> On 18/11/2019 20:00, Niek de Klein wrote:
> > Hi all,
> >
> > I am trying to have my own installation of EasyBuild,
but I
> have 3 problems:
> >
> > 1. When I try to run bootstrap.py it gives an error that
> md5sums are
> > missing, but I'm not sure where to add them as I
thought that
> should
> > then have been included in the EasyBuild-4.0.1.eb file:
> >
> > easybuild.tools.build_log.EasyBuildError: "Build of
> > /tmp/tmpfcUSAH/EasyBuild-4.0.1.eb failed (err: 'build
failed
> (first 300
> > chars): Missing checksum for
easybuild-framework-4.0.1.tar.gz')"
>
> Sorry for not responding to the GitHub issue [1] you
opened on this
> (will do so now with the answer below).
>
> We still need to clean up the bootstrap script a bit
after the
> EasyBuild
> v4.0 release, it's still doing a bunch of stuff it shouldn't
> anymore,
> and it's not compatible yet with Python 3 (see also
> https://github.com/easybuilders/easybuild-framework/pull/3028).
>
>
> Your active EasyBuild configuration has --enforce-checksums
> enabled (via
> $EASYBUILD_ENFORCE_CHECKSUMS), which explains the problem
you're
> seeing.
>
> The bootstrap script auto-generates an easyconfig file,
but it
> doesn't
> include checksums (it could I guess, with a bit more work).
>
> You can dance around this though, by temporarily
disabling the
> checksums
> requirement, only for the bootstrap:
>
> EASYBUILD_DISABLE_ENFORCE_CHECKSUMS=1 python bootstrap <path>
>
>
> If you want to, you can bootstrap EasyBuild to a temporary
> location (for
> example /tmp/$USER), and then use that installation to
pull in an
> easyconfig file for EasyBuild v4.0.1 that does have
checksums,
> using "eb
> --from-pr 9149 --installpath <final_path>" (which pulls
in the
> easyconfig from
>
https://github.com/easybuilders/easybuild-easyconfigs/pull/9149/files)
>
> for the actual installation you intend to use.
>
> >
> >
> > 2. I changed the robo and installation path to be
different,
> but I keep
> > getting "Failed to determine minimal toolchain for dep
..."
> errors. The
> > eb --show-config output is at the end of this e-mail, and
> shows that my
> > robot-paths is
> >
>
/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs/,
>
> > which is where I cloned the easyconfigs repository.
>
> What happens if you use "eb --search" with this setup,
can 'eb'
> find
> easyconfig files?
>
> Try something like "eb --search tensorflow-1.14" for example.
>
>
> >
> > 3. Even if the robo path wasn't working, tools that are
> already in my
> > module avail are not being picked up. For example,
EasyBuild
> that is not
> > working uses "toolchain = {'name': 'foss', 'version':
> '2018b'}" and has
> > as one of the dependencies "('ncurses', '6.0'),". When
I try
> to install
> > it I get
> >
> > ERROR: Failed to process easyconfig
> >
>
/groups/umcg-biogen/tmp01/tools/brain_eQTL/EasyBuild/easyconfigs/SAMtools-1.5-foss-2018b.eb:
>
> > Failed to determine minimal toolchain for dep ncurses 6.0
> >
> > but when I do ml avail ncur I get:
> >
> > ------------------------------------------------------
> > /groups/umcg-biogen/tmp01/apps/modules/devel
> > -------------------------------------------------------
> > ncurses/6.0-foss-2018b
> >
> >
>
-------------------------------------------------------------------
> > /apps/modules/devel
> >
>
-------------------------------------------------------------------
> > ncurses/6.0 ncurses/6.1-foss-2018b
> ncurses/6.1-GCCcore-7.3.0 (D)
> >
> > So the ncurses module is already available
> >
> >
> > Am I missing something in my configuration?
>
> This is a consequence of having --minimal-toolchains
enabled, which
> requires that EasyBuild is able to find the easyconfig
file for the
> toolchain (foss-2018b.eb in this case).
>
> It needs to figure out what the (versions of) the
subtoolchains
> are for
> foss/2018b, so it can check for ncurses installed with
GCCcore
> first,
> before gompi, before foss.
>
> So this is basically the same issue as with problem 2, I
bet "eb
> --search ^foss-2018b.eb" doesn't give you any result?
>
>
> Are you 100% sure the path you specified for --robot-paths is
> correct?
>
> Note that you can also prepend or append to the robot
search path
> (rather than override the default), see
>
https://easybuild.readthedocs.io/en/latest/Using_the_EasyBuild_command_line.html#controlling-robot-search-path
>
> .
>
> I hope this helps...
>
>
> regards,
>
> Kenneth
>
>
> [1]
https://github.com/easybuilders/easybuild-framework/issues/3079
>
> >
> > Thanks for your help!
> > Niek de Klein
> >
> >
> > #
> > # Current EasyBuild configuration
> > # (C: command line argument, D: default value, E:
environment
> variable,
> > F: configuration file)
> > #
> > buildpath (E) =
> > /groups/umcg-biogen/tmp01/apps//.tmp/easybuild/builds/
> > containerpath (D) =
> > /home/umcg-ndeklein/.local/easybuild/containers
> > enforce-checksums (E) = True
> > installpath (E) =
/groups/umcg-biogen/tmp01/apps/
> > minimal-toolchains (E) = True
> > repositorypath (D) =
> > /home/umcg-ndeklein/.local/easybuild/ebfiles_repo
> > robot-paths (E) =
> >
>
/groups/umcg-biogen/tmp01/apps/easybuild-easyconfigs/easybuild/easyconfigs/
> > set-gid-bit (E) = True
> > sourcepath (E) =
> /groups/umcg-biogen/tmp01/apps//sources/
> > umask (E) = 002
> > verify-easyconfig-filenames (E) = True
> >
> >
>
