Hi Tin,
On 07/10/15 03:22, tin h wrote:
Thanks folks for all the help.
--strip-componets=1 helped with the tar, but I think it is done by
default.
Well, the strip isn't done by default, but EasyBuild does notice
unpacking the sources yielded a (single) new directory, and it is smart
enough to know that it should 'cd' in there before starting the
configure/build/install cycle.
What turned out to be the root cause of my problem was that the .tgz I
created the first time had one extra level of directory, and it was
cached by EB in some tmp directory. Even after I placed a new tgz as
defined in source_urls, EB did not copy the new file to its build
cache. After manually deleting it things worked as expected.
Is there a way to force a copy of the .tgz? would "cleanupoldbuild"
remove the cache and thus always get a new .tgz?
Maybe I should file a bug on this issue?
Once EasyBuild has downloaded a source tarball, it doesn't redownload it
if it can find the file in the source path that EasyBuild was configured
to use (by default $HOME/.local/easybuild/sources).
It's not clear to me what you changed exactly, but maybe adding a
checksum for the source tarball is worth while (using "checksums =
['md5checksumhere']" in the easyconfig file). That would at least made
it clear that the source tarball was not refreshed.
W.r.t. to the 'cache' you're referring to: EasyBuild will always throw
away an existing build directory, and unpack the sources again to create
a fresh one (well, expect in the rare case where 'buildininstalldir =
True' is used in the easyconfig or easyblock).
Does this answer your question?
regards,
Kenneth
Much thanks again!
Tin
On Wed, Sep 30, 2015 at 11:51 PM, Kenneth Hoste
<[email protected] <mailto:[email protected]>> wrote:
Hi Tin,
On 01/10/15 02:32, tin h wrote:
Hello EasyBuild gurus,
Because of the workflow at my work, I am trying to install a
program using PackedBinary.
eb fails, as it complains that the sanity check files i told it
to look for isn't there. And it is not there because it created
an extra "version"directory underneath of where I expected it.
I was thinking of using install_cmd and running the tar myself,
since i wanted to preserve owners anyway. but I am not sure of
what variables i could use, where can I find such list and their
description?
I am open to other suggestions :)
I think this is what you're looking for:
$ eb -a | grep unpack_options
unpack_options Extra options for unpacking source
[default: ""]
That is, use something like:
unpack_options = '--strip-components=1'
Alternatively, you can specify the full extract command together
with the source file:
sources = [('topspin.%(version)s.tgz', "tar xfzp
--strip-components=1")]
To figure out which easyconfig parameters you can set when using a
particular easyblock, you can use "eb -a -e PackedBinary", for
example.
We're working on better documentation for the generic easyblocks
(generated from the easyblocks themselves, so we can easily keep
it up-to-date).
regards,
Kenneth
Much thanks in advance!
Tin
Here is my script:
easyblock = 'PackedBinary'
name = "topspin"
version = "3.5pl2"
description = """Topspin NMR software (data processing option
only)"""
homepage = 'http://bruker.com/'
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = ['file:///usr/prog/drop/topspin']
sources = ['topspin.%s.tgz' % version]
# for help, see eb -a -e Binary
#install_cmd = "tar xfzp" ??
postinstallcmds = [ 'touch TesT.txt', 'mkdir prog/curdir/tin']
sanity_check_paths = {
'files': ['topspin', 'cmca', 'pathScript'],
'dirs': [],
}
modextrapaths = {
'LM_LICENSE_FILE': '/prog/topspin/3.5pl2/license.dat',
'PATH': '/prog/topspin/3.5pl2',
}
modextravars = {
'TOPSPIN_HOME': '/prog/topspin/3.5pl2',
}
and here is the error message:
> eb topspin/topspin-3.5pl2.eb
== temporary log file in case of crash
/var/tmp/adm_hoti1/easybuild/tmp/easybuild-5Jm4k0/easybuild-dgyzcE.log
== resolving dependencies ...
== processing EasyBuild easyconfig
/admhome/adm_hoti1/svn/easybuild2015a/scicomp_blocks/easybuild/easyconfigs/topspin/topspin-3.5pl2.eb
== building and installing topspin/3.5pl2...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== packaging...
== postprocessing...
== sanity checking...
== FAILED: Installation ended unsuccessfully (build directory:
/var/tmp/adm_hoti1/easybuild/build/topspin/3.5pl2/dummy-dummy):
build failed (first 300 chars): EasyBuild crashed with an error
(at easybuild/framework/easyblock.py:1612 in sanity_check_step):
Sanity check failed: no file of ('topspin',) in
/clscratch/adm_hoti1/easybuild/usrProg/topspin/3.5pl2, no file of
('cmca',) in
/clscratch/adm_hoti1/easybuild/usrProg/topspin/3.5pl2, no file of
('pathScri
== Results of the build can be found in the log file
/clscratch/adm_hoti1/easybuild/tmp/easybuild-topspin-3.5pl2-20151001.013727.KKUTJ.log
ERROR: EasyBuild crashed with an error (at easybuild/main.py:112
in build_and_install_software): Build of
/admhome/adm_hoti1/svn/easybuild2015a/scicomp_blocks/easybuild/easyconfigs/topspin/topspin-3.5pl2.eb
failed (err: "build failed (first 300 chars): EasyBuild crashed
with an error (at easybuild/framework/easyblock.py:1612 in
sanity_check_step): Sanity check failed: no file of ('topspin',)
in /clscratch/adm_hoti1/easybuild/usrProg/topspin/3.5pl2, no file
of ('cmca',) in
/clscratch/adm_hoti1/easybuild/usrProg/topspin/3.5pl2, no file of
('pathScri")
EasyBuild placed the files one level too deep:
> ls -l
/clscratch/adm_hoti1/easybuild/usrProg/topspin/3.5pl2/3.5pl2/topspin*
-rwxr-xr-x 1 adm_hoti1 adm_hoti1 10602 Apr 24 01:56
/clscratch/adm_hoti1/easybuild/usrProg/topspin/3.5pl2/*3.5pl2*/topspin
