[LSST|dm-users 528] Re: Fwd: Error installing meas_base during software install
Jim Bosch
jbosch at astro.princeton.edu
Sun Dec 21 17:17:56 PST 2014
Thanks for the bug report! Knowing that this is triggered by
overly-aggressive will really help us in debugging the problem.
This is now being tracked as:
https://jira.lsstcorp.org/browse/DM-1725
I've put it on my stack for now, but that's no guarantee I'll get to it
terribly soon.
Jim
On Sat, Dec 20, 2014 at 5:12 PM, <darko at aob.rs> wrote:
>
> Hi folks.
>
> meas_base and meas_algorithms are not able to do tests on OpenSuse13.1
> with gcc version 4.8.1 20130909 [gcc-4_8-branch revision 202388] (SUSE
> Linux)
>
> Reason is to agresive optimization (-O3). -O2 doesn't work either, but I
> can report success with -O1. So the recipe is as follows
>
> when
> eups distrib install -t v10_0 lsst_distrib
>
> crashes on meas_base - open a new terminal, go to you install directory,
> do loadLSST.bash (or whatever).
> change directory to $Instal_directory/EupsBuildDir/Linux64/meas_
> base-10.0+2/
>
> do
>
> export SCONSFLAGS='opt=1'
>
> end do all the setups from build.sh - namely
>
> setup --just --type=build apr 1.3.3.lsst2
> setup --just --type=build cfitsio 3360.lsst1
> setup --just --type=build doxygen 1.8.5
> setup --just --type=build eigen 3.2.0
> setup --just --type=build fftw 3.3.3
> setup --just --type=build gsl 1.16.lsst1
> setup --just --type=build minuit2 5.28.00
> setup --just --type=build mysql 5.1.65.lsst1
> setup --just --type=build mysqlclient 5.1.73.lsst1
> setup --just --type=build python 0.0.2
> setup --just --type=build sqlite 3080200
> setup --just --type=build swig 3.0.2.lsst1
> setup --just --type=build xpa 2.1.15.lsst1
> setup --just --type=build apr_util 1.3.4.lsst2
> setup --just --type=build boost 1.55.0.1.lsst2
> setup --just --type=build mysqlpython 1.2.3+13
> setup --just --type=build numpy 0.0.1+2
> setup --just --type=build scons 2.3.0+1
> setup --just --type=build wcslib 4.14+7
> setup --just --type=build activemqcpp 3.5.0+15
> setup --just --type=build astrometry_net 0.50.1+3
> setup --just --type=build matplotlib 0.0.1+2
> setup --just --type=build pyfits 3.2.4.lsst1
> setup --just --type=build scisql 0.3.4+2
> setup --just --type=build sconsUtils 10.0
> setup --just --type=build astrometry_net_data 10.0+1
> setup --just --type=build base 10.0+2
> setup --just --type=build geom 10.0+1
> setup --just --type=build lsst 10.0
> setup --just --type=build lsst_thirdparty 10.0+2
> setup --just --type=build ndarray 10.0+1
> setup --just --type=build pex_exceptions 10.0+1
> setup --just --type=build utils 10.0+1
> setup --just --type=build daf_base 10.0+2
> setup --just --type=build pex_logging 10.0+1
> setup --just --type=build pex_policy 10.0+1
> setup --just --type=build daf_persistence 10.0+2
> setup --just --type=build pex_config 10.0+1
> setup --just --type=build afw 10.0+3
> setup --just --type=build cat 10.0+2
> setup --just --type=build lsst_libs 10.0+2
> setup --just --type=build ctrl_events 10.0+4
> setup --just --type=build ctrl_provenance 10.0+5
> setup --just --type=build shapelet 10.0+2
> setup --just --type=build skymap 10.0+2
> setup --just --type=build skypix 10.0+2
> setup --just --type=build daf_butlerUtils 10.0+3
> setup --just --type=build pex_harness 10.0+7
> setup --just --type=build ctrl_orca 10.0+8
> setup --just --type=build obs_test 10.0+2
> setup --just --type=build ctrl_execute 10.0+8
> setup --just --type=build pipe_base 10.0+2
> setup --just --type=build testing_endtoend 10.0+7
> setup --just --type=build coadd_utils 10.0+3
> setup --just --type=build ctrl_platform_gordon 10.0+8
> setup --just --type=build ctrl_platform_lsst 10.0+8
> setup --just --type=build coadd_chisquared 10.0+3
>
>
> after that change directory to
>
> $Instal_directory/EupsBuildDir/Linux64/meas_base-10.0+2/meas_base-10.0+2
>
> and do
>
> setup --type=build -k -r
>
> ./ups/eupspkg VERBOSE=0 FLAVOR=Linux64 config
> ./ups/eupspkg VERBOSE=0 FLAVOR=Linux64 build
> ./ups/eupspkg VERBOSE=0 FLAVOR=Linux64 install
>
>
> If everything goes fine then from your original terminal/window do
>
> eups declare meas_base 10.0+2 -r $Instal_directory/Linux64/meas_base/10.0+2
> -t current
>
> eups declare meas_base 10.0+2 -r $Instal_directory/Linux64/meas_base/10.0+2
> -t v10_0
>
> restart instalation
>
>
> Now, meas_algorithms will probably die as well (same recipe):
>
> In terminal you were using to manualy build go to $Instal_directory/
> EupsBuildDir/Linux64/meas_algorithms-10.0+2
>
> do just one new setup (others are already done)
>
> setup --just --type=build meas_base 10.0+2
>
> change directory to
>
> $Instal_directory/EupsBuildDir/Linux64/meas_algorithms-10.0+2/meas_
> algorithms-10.0+2
>
> do
>
> setup --type=build -k -r
>
> ./ups/eupspkg VERBOSE=0 FLAVOR=Linux64 config
> ./ups/eupspkg VERBOSE=0 FLAVOR=Linux64 build
> ./ups/eupspkg VERBOSE=0 FLAVOR=Linux64 install
>
>
> Now from the original terminal do eups declare step
>
> eups declare meas_base 10.0+2 -r $Instal_directory/Linux64/meas_algorithms/10.0+2
> -t current
>
> eups declare meas_base 10.0+2 -r $Instal_directory/Linux64/meas_algorithms/10.0+2
> -t v10_0
>
>
> and restart installation (this should go smoothly till the end)
>
> Hope this helps in sorting out problems with meas_base and meas_algorithms
> on other distributions as well.
>
> Someone should check why this happens and maybe offer more elegant
> solution...
>
> Cheers
> D.
>
>
> On Tue, 9 Dec 2014, Mario Juric wrote:
>
> Hi Mike,
>> CentOS 6 is supported (it's out default/reference platform). What problem
>> are you seeing building on CentOS?
>> --
>> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>>
>> On December 8, 2014 3:55:51 PM PST, Mike Lund <mike.lund at gmail.com>
>> wrote:
>> Thanks for all that information, at the present I have the poor
>> luck of the other machine I've got access to running CentOS 6.6, which is
>> also not supported at this time, so I'll be
>> watching for support being extended to Ubuntu 14.04 or CentOS 6.6
>> so that I can complete and installation and resume working with MAF again.
>>
>> I'm definitely also willing to try out any other distribution
>> methods that are being explored as a guinea pig of sorts, although from
>> looking at CernVM-FS, it seems like Fabio
>> wouldn't have much need of that for that implementation.
>>
>> - Mike Lund
>>
>> On Mon, Dec 8, 2014 at 1:27 PM, Dominique Boutigny <boutigny at in2p3.fr>
>> wrote:
>> Hi Mike,
>>
>> I am also using a Ubuntu 14.04 system and I am having the same
>> problem as you. So, what I am doing is to build the stack on another
>> platform (I use Scientic Linux / Redhat)
>> and simply make a tar ball that I deploy on my system. This is
>> working very well, you only have to fix a couple of things for eups.
>> Here is a copy of the recipe I put in the IN2P3 wiki :
>> http://lsst.in2p3.fr/wiki/index.php/Calcul (you can create an account
>> for yourself, it is not moderated).
>>
>> Hope this helps
>>
>> Dominique
>>
>> PS : Fabio Hernandez at CC-IN2P3 is also working on a system to
>> deploy the LSST stack using CernVM-FS. This is very convenient. You can
>> contact him directly if you wish.
>>
>> INTRODUCTION
>>
>> It is possible to replicate a working stack installation into
>> another directory structure or even on another computer without recompiling
>> the packages. Here is how to proceed,
>> taking the example of the stack v9_2 installed at CC-IN2P3 :
>>
>> cd /sps/lsst/Library/stack_v9_2
>> tar -cvzf stack.tar.gz *
>>
>> cp stack.tar.gz some_directory (on the same or on another server)
>>
>> tar -xvzf stack.tar.gz
>>
>> At this stage we have the stack directory structure but in order to
>> make it work, we need to fix the following :
>>
>> o Cleanup any LSST or EUPS environment variable (it may be safer
>> to start a completely new shell)
>> o Change LSST_HOME in loadLSST.sh
>> o Change EUPS_DIR and EUPS_PATH in eups/bin/setups.sh
>>
>> Then one can now re-initialize the stack environment :
>>
>> source loadLSST.sh
>>
>> The eups database should now be ok.
>>
>> [MODIFIER]CAVEATS
>>
>> [modifier]Fixing eups for some manually declared packages
>>
>> If some packages have been manually declared to eups without
>> specifying a path relative to EUPS_PATH, one have to undeclare those
>> packages in order to re-declare them with the
>> right path. For instance :
>>
>> unsetup obs_cfht my_obs_cfht
>> eups undeclare obs_cfht my_obs_cfht
>> eups declare -r some_directory/my_packages/obs_cfht obs_cfht my_obs_cfht
>> setup obs_cfht my_obs_cfht
>>
>> [modifier]Fixing ipython
>>
>> If the stack release comes with the anaconda python distribution,
>> the firs line of the ipython wrap-up script should be fixed to point to the
>> right python path.
>>
>> [MODIFIER]REMARK
>>
>>
>> This method is working to install the stack on Ubuntu 14.04 by
>> copying the stack from a SL6.5 distribution
>>
>> On 12/08/2014 11:17 AM, Mike Lund wrote:
>> Dominique, thanks for the quick answer on this.
>>
>> To follow this up with a probably naive question, are there any
>> options to get this working other than the stack build? If it effects
>> anything, my needs for the software
>> are primarily just for writing new metrics for the MAF. I also know
>> that Ubuntu 14.10 is out now, and that is something that I could upgrade to
>> if the issues with gcc
>> are limited to just 14.04 and not later versions.
>> - Mike Lund
>>
>> On Sat, Dec 6, 2014 at 1:12 PM, Dominique Boutigny <boutigny at in2p3.fr>
>> wrote:
>> Hi Mike,
>>
>> Until recently, the stack build was incompatible with Ubuntu 14.04
>> due to some gcc subtleties. So, unless this was fixed in the mean time,
>> this is likely the
>> reason of the errors that you are seeing.
>>
>> Best,
>>
>> Dominique
>> On 12/6/2014 11:03 AM, Mike Lund wrote:
>> Hello, Lynne Jones recommended I send this question to here and
>> thanks in advance for any help.
>>
>> I'm trying to install the LSST software, and my install is failing
>> when trying to meas_base, and the screen output is saying that it's running
>> python test
>> scripts and failing 15 tests. I'm trying to install this on Ubuntu
>> 14.04.1 LTS, and the last few lines output to terminal are the following:
>>
>> scons: *** [checkTestStatus] Error 1
>> scons: building terminated because of errors.
>> + exit -4
>> eups distrib: Failed to build meas_base-master-g5cbca8985d.eupspkg:
>> Command:
>> source /home/mike/lsst/eups/bin/setups.sh; export
>> EUPS_PATH=/home/mike/lsst; (/home/mike/lsst/EupsBuildDir/
>> Linux64/meas_base-master-g5cbca8985d/build.sh) >>
>> /home/mike/lsst/EupsBuildDir/Linux64/meas_base-master-g5cbca8985d/build.log
>> 2>&1 4>/home/mike/lsst/EupsBuildDir/Linux64/meas_
>> base-master-g5cbca8985d/build.msg
>> exited with code 252
>>
>> I've also attached the build.log for this.
>>
>> - Mike Lund
>>
>>
>>
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>>
>> --
>> Dominique Boutigny - CNRS / CC-IN2P3
>> Now at SLAC National Accelerator Laboratory
>>
>> Mail : boutigny at in2p3.fr - boutigny at slac.stanford.edu
>> Office : +1 650-926-5759 - Cellular : +1 774-232-0912
>> _______________________________________________
>> dm-users mailing list
>> dm-users at lists.lsst.org
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>>
>>
>>
>> --
>> Dominique Boutigny - CNRS / CC-IN2P3
>> Now at SLAC National Accelerator Laboratory
>>
>> Kavli Building - Room 221
>> Mail : boutigny at in2p3.fr - boutigny at slac.stanford.edu
>> Office : +1 650-926-5759 - Cellular : +1 774-232-0912
>>
>>
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