Test Toolshed Biopython package dependency Atlas fails to install (Was: Re: UnboundLocalError: local variable 'prior_installation_required' referenced before assignment)
On Thu, Sep 19, 2013 at 5:15 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time both repositories fail with the same error. I guess before something was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition: http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I can confirm biopython repository is failing to install for me with exactly the same error. I wonder if a recently addition in the test toolshed broke the treatment of "prior_installation_required".
Thanks, Carlos
Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already...
I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry.
In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log x ATLAS/tune/lapack/lanbsrch.c tar: Error exit delayed from previous errors. ############################################# This is the relevant part I can find in Galaxy's log: [localhost] local: tar xfvj atlas3.10.1.tar.bz2 Warning: local() encountered an error (return code 1) while executing 'tar xfvj atlas3.10.1.tar.bz2' After noticing this I got what I'm guessing is the original file from sourceforge: http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.... I can confirm that trying to untar this file fails with the exact same error. However, on Ubuntu 13.04 untaring this file works just fine. On Ubuntu 13.04 the error I see is: STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information ############################################# Björn, you said cpu throttling can be easily disable on Ubuntu. Can you comment how? Do I need to disable it completely, or should the install script do it when installing? Thanks, Carlos
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time both repositories fail with the same error. I guess before something was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition: http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I can confirm biopython repository is failing to install for me with exactly the same error. I wonder if a recently addition in the test toolshed broke the treatment of "prior_installation_required".
Thanks, Carlos
Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already...
I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry.
In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log x ATLAS/tune/lapack/lanbsrch.c tar: Error exit delayed from previous errors. #############################################
This is the relevant part I can find in Galaxy's log: [localhost] local: tar xfvj atlas3.10.1.tar.bz2
Warning: local() encountered an error (return code 1) while executing 'tar xfvj atlas3.10.1.tar.bz2'
After noticing this I got what I'm guessing is the original file from sourceforge: http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10....
I can confirm that trying to untar this file fails with the exact same error. However, on Ubuntu 13.04 untaring this file works just fine.
That is new to me. How can that happen? Anyone with an OS-X can confirm that?
On Ubuntu 13.04 the error I see is: STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information #############################################
Björn, you said cpu throttling can be easily disable on Ubuntu. Can you comment how? Do I need to disable it completely, or should the install script do it when installing?
ATLAS (once untared ;-)) needs cpu-throttling to be disabled to optimizes its library. If it is not disabled ATLAS compilation will fail. For OS-X I found that: http://apple.stackexchange.com/questions/41045/how-can-i-disable-cpu-throttl... Sorry, I never touched a OS-X. Nevertheless, If its not disabled, it is supposed to fail silently and downstream packages will not be affected. But if its crashing during untarring, I can't do much. What I can do is to repack the tarball and host it elsewhere. What brings me to: http://gmod.827538.n3.nabble.com/RFC-Storing-of-tarballs-and-patches-for-too... Bad news for a Friday morning, sorry :( Bjoern
Thanks, Carlos
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Yes this tar is broken at least on OSX. Other people have the same issue: http://code.google.com/p/libarchive/issues/detail?id=299 On Sep 20, 2013, at 10:41 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time both repositories fail with the same error. I guess before something was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition: http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I can confirm biopython repository is failing to install for me with exactly the same error. I wonder if a recently addition in the test toolshed broke the treatment of "prior_installation_required".
Thanks, Carlos
Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already...
I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry.
In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log x ATLAS/tune/lapack/lanbsrch.c tar: Error exit delayed from previous errors. #############################################
This is the relevant part I can find in Galaxy's log: [localhost] local: tar xfvj atlas3.10.1.tar.bz2
Warning: local() encountered an error (return code 1) while executing 'tar xfvj atlas3.10.1.tar.bz2'
After noticing this I got what I'm guessing is the original file from sourceforge: http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10....
I can confirm that trying to untar this file fails with the exact same error. However, on Ubuntu 13.04 untaring this file works just fine.
That is new to me. How can that happen? Anyone with an OS-X can confirm that?
On Ubuntu 13.04 the error I see is: STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information #############################################
Björn, you said cpu throttling can be easily disable on Ubuntu. Can you comment how? Do I need to disable it completely, or should the install script do it when installing?
ATLAS (once untared ;-)) needs cpu-throttling to be disabled to optimizes its library. If it is not disabled ATLAS compilation will fail. For OS-X I found that:
http://apple.stackexchange.com/questions/41045/how-can-i-disable-cpu-throttl...
Sorry, I never touched a OS-X. Nevertheless, If its not disabled, it is supposed to fail silently and downstream packages will not be affected. But if its crashing during untarring, I can't do much. What I can do is to repack the tarball and host it elsewhere. What brings me to:
http://gmod.827538.n3.nabble.com/RFC-Storing-of-tarballs-and-patches-for-too...
Bad news for a Friday morning, sorry :( Bjoern
Thanks, Carlos
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Thanks for posting that Ido, Right now I would suggest manually installing these dependencies, rather than ticking the box for the Tool Shed to do it for you. If you are using the Apple provided Python to run your Galaxy on Mac OS X, it comes with NumPy anyway, so compiling Biopython should be simple (just install XCode and the command line tools first). Note that I have not yet updated my Biopython using tools on the main tool shed to include the automatic dependency on the Tool Shed Biopython package, so they require a manual install for now. As soon as the NumPy/ATLAS packaging issue is solved, I plan to push those updates from the Test Tool Shed though. Peter On Fri, Sep 20, 2013 at 10:04 AM, Ido Tamir <tamir@imp.ac.at> wrote:
Yes this tar is broken at least on OSX. Other people have the same issue: http://code.google.com/p/libarchive/issues/detail?id=299
On Sep 20, 2013, at 10:41 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time both repositories fail with the same error. I guess before something was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition: http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I can confirm biopython repository is failing to install for me with exactly the same error. I wonder if a recently addition in the test toolshed broke the treatment of "prior_installation_required".
Thanks, Carlos
Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already...
I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry.
In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log x ATLAS/tune/lapack/lanbsrch.c tar: Error exit delayed from previous errors. #############################################
This is the relevant part I can find in Galaxy's log: [localhost] local: tar xfvj atlas3.10.1.tar.bz2
Warning: local() encountered an error (return code 1) while executing 'tar xfvj atlas3.10.1.tar.bz2'
After noticing this I got what I'm guessing is the original file from sourceforge: http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10....
I can confirm that trying to untar this file fails with the exact same error. However, on Ubuntu 13.04 untaring this file works just fine.
That is new to me. How can that happen? Anyone with an OS-X can confirm that?
On Ubuntu 13.04 the error I see is: STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information #############################################
Björn, you said cpu throttling can be easily disable on Ubuntu. Can you comment how? Do I need to disable it completely, or should the install script do it when installing?
ATLAS (once untared ;-)) needs cpu-throttling to be disabled to optimizes its library. If it is not disabled ATLAS compilation will fail. For OS-X I found that:
http://apple.stackexchange.com/questions/41045/how-can-i-disable-cpu-throttl...
Sorry, I never touched a OS-X. Nevertheless, If its not disabled, it is supposed to fail silently and downstream packages will not be affected. But if its crashing during untarring, I can't do much. What I can do is to repack the tarball and host it elsewhere. What brings me to:
http://gmod.827538.n3.nabble.com/RFC-Storing-of-tarballs-and-patches-for-too...
Bad news for a Friday morning, sorry :( Bjoern
Thanks, Carlos
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Hi Ido and Carlos, can you check if that tarball is working? http://downloads.sourceforge.net/project/math-atlas/Developer%20% 28unstable%29/3.11.11/atlas3.11.11.tar.bz2 The chance is low, but if its working for you I will consider to create a new version for it. Thanks, Bjoern
Yes this tar is broken at least on OSX. Other people have the same issue: http://code.google.com/p/libarchive/issues/detail?id=299
On Sep 20, 2013, at 10:41 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time both repositories fail with the same error. I guess before something was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition: http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I can confirm biopython repository is failing to install for me with exactly the same error. I wonder if a recently addition in the test toolshed broke the treatment of "prior_installation_required".
Thanks, Carlos
Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already...
I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry.
In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log x ATLAS/tune/lapack/lanbsrch.c tar: Error exit delayed from previous errors. #############################################
This is the relevant part I can find in Galaxy's log: [localhost] local: tar xfvj atlas3.10.1.tar.bz2
Warning: local() encountered an error (return code 1) while executing 'tar xfvj atlas3.10.1.tar.bz2'
After noticing this I got what I'm guessing is the original file from sourceforge: http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10....
I can confirm that trying to untar this file fails with the exact same error. However, on Ubuntu 13.04 untaring this file works just fine.
That is new to me. How can that happen? Anyone with an OS-X can confirm that?
On Ubuntu 13.04 the error I see is: STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information #############################################
Björn, you said cpu throttling can be easily disable on Ubuntu. Can you comment how? Do I need to disable it completely, or should the install script do it when installing?
ATLAS (once untared ;-)) needs cpu-throttling to be disabled to optimizes its library. If it is not disabled ATLAS compilation will fail. For OS-X I found that:
http://apple.stackexchange.com/questions/41045/how-can-i-disable-cpu-throttl...
Sorry, I never touched a OS-X. Nevertheless, If its not disabled, it is supposed to fail silently and downstream packages will not be affected. But if its crashing during untarring, I can't do much. What I can do is to repack the tarball and host it elsewhere. What brings me to:
http://gmod.827538.n3.nabble.com/RFC-Storing-of-tarballs-and-patches-for-too...
Bad news for a Friday morning, sorry :( Bjoern
Thanks, Carlos
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
tar xvfj atlas3.11.11.tar.bz2 shows no errors on OSX and creates one ATLAS folder. best, ido On Sep 20, 2013, at 11:17 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Ido and Carlos,
can you check if that tarball is working?
http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%...
The chance is low, but if its working for you I will consider to create a new version for it. Thanks, Bjoern
Yes this tar is broken at least on OSX. Other people have the same issue:
http://code.google.com/p/libarchive/issues/detail?id=299
On Sep 20, 2013, at 10:41 AM, Bjoern Gruening < bjoern.gruening@gmail.com
wrote:
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote: > I did an extra test. Started with a clean 'galaxy-dist'. This time > both repositories fail with the same error. I guess before something > was cached for the repository with version 0.1.4. > > I used biopython repository as a guide to write my tool dependency definition: > http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 > > I can confirm biopython repository is failing to install for me with > exactly the same error. I wonder if a recently addition in the test > toolshed broke the treatment of "prior_installation_required". > > Thanks, > Carlos
Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already...
I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry.
In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log x ATLAS/tune/lapack/lanbsrch.c tar: Error exit delayed from previous errors. #############################################
This is the relevant part I can find in Galaxy's log: [localhost] local: tar xfvj atlas3.10.1.tar.bz2
Warning: local() encountered an error (return code 1) while executing 'tar xfvj atlas3.10.1.tar.bz2'
After noticing this I got what I'm guessing is the original file from sourceforge: http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10....
I can confirm that trying to untar this file fails with the exact same error. However, on Ubuntu 13.04 untaring this file works just fine.
That is new to me. How can that happen? Anyone with an OS-X can confirm that?
On Ubuntu 13.04 the error I see is: STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information #############################################
Björn, you said cpu throttling can be easily disable on Ubuntu. Can you comment how? Do I need to disable it completely, or should the install script do it when installing?
ATLAS (once untared ;-)) needs cpu-throttling to be disabled to optimizes its library. If it is not disabled ATLAS compilation will fail. For OS-X I found that:
http://apple.stackexchange.com/questions/41045/how-can-i-disable-cpu-throttl...
Sorry, I never touched a OS-X. Nevertheless, If its not disabled, it is supposed to fail silently and downstream packages will not be affected. But if its crashing during untarring, I can't do much. What I can do is to repack the tarball and host it elsewhere. What brings me to:
http://gmod.827538.n3.nabble.com/RFC-Storing-of-tarballs-and-patches-for-too...
Bad news for a Friday morning, sorry :( Bjoern
Thanks, Carlos
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
On Fri, Sep 20, 2013 at 10:17 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Ido and Carlos,
can you check if that tarball is working?
http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%...
The chance is low, but if its working for you I will consider to create a new version for it. Thanks, Bjoern
Hi Bjoern, That archive file works for me on Mac OS X 10.8.5, details below. Peter -- I was fooled for a moment, it is one of the annoying SourceForge URLs which doesn't work at the command line - their mirror system is horrid: $ curl -O http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 So, getting a real link via my browser: $ curl -O http://kent.dl.sourceforge.net/project/math-atlas/Developer%20%28unstable%29... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 5115k 100 5115k 0 0 1267k 0 0:00:04 0:00:04 --:--:-- 1272k $ tar -jxvf atlas3.11.11.tar.bz2 ... $ cd ATLAS/ $ ./configure ATLAS can no longer be configured in the exact source directory, create a subdir such as MyObj. See ATLAS/INSTALL.txt for help. $ mkdir my_build_dir ; cd my_build_dir $ ../configure gcc -I/tmp/x/ATLAS/my_build_dir/..//CONFIG/include -g -w -c /tmp/x/ATLAS/my_build_dir/..//CONFIG/src/atlconf_misc.c gcc -I/tmp/x/ATLAS/my_build_dir/..//CONFIG/include -g -w -o xconfig /tmp/x/ATLAS/my_build_dir/..//CONFIG/src/config.c atlconf_misc.o ./xconfig -d s /tmp/x/ATLAS/my_build_dir/../ -d b /tmp/x/ATLAS/my_build_dir OS configured as OSX (12) Assembly configured as GAS_x8664 (2) Vector ISA Extension configured as SSE3 (6,448) Architecture configured as Core2 (25) Clock rate configured as 2800Mhz Maximum number of threads configured as 8 Parallel make command configured as '$(MAKE) -j 8' Cannot detect CPU throttling. ... $ time make make -f Make.top build cd bin/ ; make xatlas_build /usr/bin/gcc -DL2SIZE=33554432 -I/tmp/x/ATLAS/my_build_dir/include -I/tmp/x/ATLAS/my_build_dir/..//include -I/tmp/x/ATLAS/my_build_dir/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Core2 -DATL_CPUMHZ=2800 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -m64 -DATL_NCPU=8 -O -fomit-frame-pointer -m64 -c /tmp/x/ATLAS/my_build_dir/..//bin/atlas_tee.c /usr/bin/gcc -DL2SIZE=33554432 -I/tmp/x/ATLAS/my_build_dir/include -I/tmp/x/ATLAS/my_build_dir/..//include -I/tmp/x/ATLAS/my_build_dir/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Core2 -DATL_CPUMHZ=2800 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -m64 -DATL_NCPU=8 -O -fomit-frame-pointer -m64 -o xatlas_tee atlas_tee.o ... cc1: error: unrecognized command line option "-mcpu=ultrasparc" FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch cc1: error: unrecognized command line option "-maltivec" cc1: error: unrecognized command line option "-mabi=altivec" cc1: error: unrecognized command line option "-mcpu=ultrasparc" cc1: error: unrecognized command line option "-mcpu=ultrasparc" cc1: error: unrecognized command line option "-mcpu=ultrasparc" cc1: error: unrecognized command line option "-mcpu=970" cc1: error: unrecognized command line option "-mips4" cc1: error: unrecognized command line option "-mips4" cc1: error: unrecognized command line option "-mips4" cc1: error: unrecognized command line option "-mips4" cc1: error: unrecognized command line option "-mvsx" cc1: error: unrecognized command line option "-mfpu=vfpv3" ... ATLAS install complete. Examine ATLAS/bin/<arch>/INSTALL_LOG/SUMMARY.LOG for details. make clean rm -rf *.dSYM rm -f *.o x* config?.out *core* real 8m35.518s user 7m33.738s sys 2m17.387s $ time make test ... 8 cases: 8 passed, 0 skipped, 0 failed 4 cases: 4 passed, 0 skipped, 0 failed 8 cases: 8 passed, 0 skipped, 0 failed 4 cases: 4 passed, 0 skipped, 0 failed 8 cases: 8 passed, 0 skipped, 0 failed 4 cases: 4 passed, 0 skipped, 0 failed 8 cases: 8 passed, 0 skipped, 0 failed 4 cases: 4 passed, 0 skipped, 0 failed DONE SCOPING FOR FAILURES IN CBLAS TESTS: fgrep -e fault -e FAULT -e error -e ERROR -e fail -e FAIL \ interfaces/blas/C/testing/sanity.out | \ fgrep -v PASSED make[1]: [sanity_test] Error 1 (ignored) DONE SCOPING FOR FAILURES IN F77BLAS TESTS: fgrep -e fault -e FAULT -e error -e ERROR -e fail -e FAIL \ interfaces/blas/F77/testing/sanity.out | \ fgrep -v PASSED make[1]: [sanity_test] Error 1 (ignored) DONE real 0m38.065s user 0m27.856s sys 0m6.329s
Hi, I tried to things to solve it. 1: I uploaded a new version to: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time with target_filename="ATLAS.tar.bz2". That is a rather new feature, so you will need a recent Galaxy version. The prosite is that we do not need to call 'tar', we are using the python tarfile module. Hopefully that will work, also on OS-X 2: I have created: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_11 Peter was able to install it on OS-X, at least on commandline, so I have hope that this one is working, well. The downside is, that it is a unstable version and will disappear from the server. Would be great if you can give both a try. For me its working. That means on ubuntu its installed and on Fedora its failing silently with 'It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information'. Thanks for your help! Bjoern
On Thu, Sep 19, 2013 at 5:15 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time both repositories fail with the same error. I guess before something was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition: http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I can confirm biopython repository is failing to install for me with exactly the same error. I wonder if a recently addition in the test toolshed broke the treatment of "prior_installation_required".
Thanks, Carlos
Could be - note that currently Biopython isn't currently installing properly on the Test Tool Shed due to ALTAS failing (a requirement of NumPy which is a requirement of Biopython). Dave and Bjoern are I think looking at this already...
I can't do much I tested it again and for me its working fine on my computers I have at hand ... sorry.
In case it helps, this is how the INSTALLATION.log file ends on OS X 10.8.4: $ tail -n 3 ~/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/3508de0ebae1/INSTALLATION.log x ATLAS/tune/lapack/lanbsrch.c tar: Error exit delayed from previous errors. #############################################
This is the relevant part I can find in Galaxy's log: [localhost] local: tar xfvj atlas3.10.1.tar.bz2
Warning: local() encountered an error (return code 1) while executing 'tar xfvj atlas3.10.1.tar.bz2'
After noticing this I got what I'm guessing is the original file from sourceforge: http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10....
I can confirm that trying to untar this file fails with the exact same error. However, on Ubuntu 13.04 untaring this file works just fine.
On Ubuntu 13.04 the error I see is: STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information #############################################
Björn, you said cpu throttling can be easily disable on Ubuntu. Can you comment how? Do I need to disable it completely, or should the install script do it when installing?
Thanks, Carlos
On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi,
I tried to things to solve it.
Was this specifically to solve ATLAS under Mac OS X, or more generally include the problem shown on the Galaxy (Test) Tool Shed?
1: I uploaded a new version to: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time with target_filename="ATLAS.tar.bz2". That is a rather new feature, so you will need a recent Galaxy version. The prosite is that we do not need to call 'tar', we are using the python tarfile module. Hopefully that will work, also on OS-X
Not tried.
2: I have created: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_11 Peter was able to install it on OS-X, at least on commandline, so I have hope that this one is working, well. The downside is, that it is a unstable version and will disappear from the server.
Tried on a CentOS machine (running galaxy-central), it appeared to work but on closer inspection: Missing tool dependencies - click the name to install the missing dependency Name Version Type Installation status atlas 3.11.11 package Error $ cat /opt/galaxy-dist-shed-tools/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/INSTALLATION.log ############################################# # try to disable cpu throttling if hash cpufreq-selector 2>/dev/null; then cpufreq-selector -g performance elif hash cpupower 2>/dev/null; then cpupower frequency-set -g performance else echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' exit fi STDOUT ############################################# ############################################# # try to disable cpu throttling if hash cpufreq-selector 2>/dev/null; then cpufreq-selector -g performance elif hash cpupower 2>/dev/null; then cpupower frequency-set -g performance else echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' exit fi STDERR You must be root #############################################
Would be great if you can give both a try. For me its working. That means on ubuntu its installed and on Fedora its failing silently with 'It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information'.
Like Fedora, on CentOS I am getting a silent failure :( Peter
On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi,
I tried to things to solve it.
Was this specifically to solve ATLAS under Mac OS X, or more generally include the problem shown on the Galaxy (Test) Tool Shed?
Yes. My hope was to use tarfile from python and not 'tar', because bsdtar seems to crash with that package.
1: I uploaded a new version to: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time with target_filename="ATLAS.tar.bz2". That is a rather new feature, so you will need a recent Galaxy version. The prosite is that we do not need to call 'tar', we are using the python tarfile module. Hopefully that will work, also on OS-X
Not tried.
2: I have created: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_11 Peter was able to install it on OS-X, at least on commandline, so I have hope that this one is working, well. The downside is, that it is a unstable version and will disappear from the server.
Tried on a CentOS machine (running galaxy-central), it appeared to work but on closer inspection:
Missing tool dependencies - click the name to install the missing dependency Name Version Type Installation status atlas 3.11.11 package Error
$ cat /opt/galaxy-dist-shed-tools/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/INSTALLATION.log
#############################################
# try to disable cpu throttling if hash cpufreq-selector 2>/dev/null; then cpufreq-selector -g performance elif hash cpupower 2>/dev/null; then cpupower frequency-set -g performance else echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' exit fi
STDOUT
#############################################
#############################################
# try to disable cpu throttling if hash cpufreq-selector 2>/dev/null; then cpufreq-selector -g performance elif hash cpupower 2>/dev/null; then cpupower frequency-set -g performance else echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' exit fi
STDERR You must be root #############################################
Would be great if you can give both a try. For me its working. That means on ubuntu its installed and on Fedora its failing silently with 'It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information'.
Like Fedora, on CentOS I am getting a silent failure :(
For whatever reason I get the following in my log. Galaxy tries to continue with the installation, that fine. But in your case Galaxy aborts. Nevertheless, failing silently means, that biopython and numpy will not be affected (hopefully). I can also remove the manuell deactivation of cpu throttling, it was just an idea to support more systems out of the box without admin invention. ############################################# # try to disable cpu throttling if hash cpufreq-selector 2>/dev/null; then cpufreq-selector -g performance elif hash cpupower 2>/dev/null; then cpupower frequency-set -g performance else echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' exit fi STDOUT ############################################# ############################################# # try to disable cpu throttling if hash cpufreq-selector 2>/dev/null; then cpufreq-selector -g performance elif hash cpupower 2>/dev/null; then cpupower frequency-set -g performance else echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' exit fi STDERR Error calling SetGovernor: Caller is not authorized ############################################# ############################################# mkdir build && cd build && mkdir /home/gruening/projects/code/galaxy-central/tool_deps/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/atlas/ && ../configure -Fa alg -fPIC --prefix=/home/gruening/projects/code/galaxy-central/tool_deps/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/atlas/ --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz STDOUT gcc -I/home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/..//CONFIG/include -g -w -c /home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/..//CONFIG/src/atlconf_misc.c gcc -I/home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/..//CONFIG/include -g -w -o xconfig /home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/..//CONFIG/src/config.c atlconf_misc.o ./xconfig -d s /home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build/../ -d b /home/gruening/projects/code/galaxy-central/database/tmp/tmp-toolshed-mtdfjNMLM/ATLAS/build -Fa alg -fPIC -Si lapackref 1 OS configured as Linux (1) Assembly configured as GAS_x8664 (2) Vector ISA Extension configured as AVX (5,480) Architecture configured as Corei2 (27) Clock rate configured as 1600Mhz Maximum number of threads configured as 4 Parallel make command configured as '$(MAKE) -j 4' CPU Throttling apparently enabled! xconfig exited with 1 ############################################# ############################################# mkdir build && cd build && mkdir /home/gruening/projects/code/galaxy-central/tool_deps/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/atlas/ && ../configure -Fa alg -fPIC --prefix=/home/gruening/projects/code/galaxy-central/tool_deps/atlas/3.11.11/iuc/package_atlas_3_11/3e1635c33e26/atlas/ --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz STDERR It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information #############################################
Peter
On Fri, Sep 20, 2013 at 8:48 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi,
I tried to things to solve it.
1: I uploaded a new version to: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time with target_filename="ATLAS.tar.bz2". That is a rather new feature, so you will need a recent Galaxy version. The prosite is that we do not need to call 'tar', we are using the python tarfile module. Hopefully that will work, also on OS-X
2: I have created: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_11 Peter was able to install it on OS-X, at least on commandline, so I have hope that this one is working, well. The downside is, that it is a unstable version and will disappear from the server.
Would be great if you can give both a try. For me its working. That means on ubuntu its installed and on Fedora its failing silently with 'It appears you have cpu throttling enabled, which makes timings unreliable and an ATLAS install nonsensical. Aborting. See ATLAS/INSTALL.txt for further information'.
I don't have access to my OS X box until later tonight. On Ubuntu with an up-to-date instance of galaxy-central is failing now for me with a different error: STDOUT ./xconfig -d s /home/cborroto/src/galaxy-central/database/tmp/tmp-toolshed-mtdyWTv64/ATLAS/build/../ -d b /home/cborroto/src/galaxy-central/database/tmp/tmp-toolshed-mtdyWTv64/ATLAS/build -Fa alg -fPIC -Si lapa ckref 1 xconfig exited with 127 ############################################# ############################################# mkdir build && cd build && mkdir /home/cborroto/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/d32504e1aea8/atlas/ && ../configure -Fa alg -fPIC --prefix=/home/cborroto/src/shed_tools_dependencies.central/atlas/3.10.1/iuc/package_atlas_3_10/d32504e1aea8/atlas/ --with-netlib-lapack-tarfile=../lapack-3.4.2.tgz STDERR cat: ..//CONFIG/src/Makefile: No such file or directory cp: cannot stat ‘..//CONFIG/src/atlcomp.txt’: No such file or directory make: *** No rule to make target `xconfig'. Stop. /bin/sh: 1: ./xconfig: not found Full INSTALLATION.log: http://pastebin.com/raw.php?i=hvqFWvgJ Somehow this is also a silent failing and numpy, biopython and ngs-tools(my tool package depending on biopython) get "Installed"(Green) while lapack, atlas and split_by_barcode(my actual tool wrapper depending on ngs-tools package) get "Installed, missing tool dependencies"(Grey). This means if I try to use my wrapper in this state I get this error: /bin/sh: 1: ngs-tools: not found However, if I do a "Repair repository" on split_by_barcode it goes into "Installed"(Green) and everything seems to work from then on. Thanks for working on this, Carlos
participants (4)
-
Bjoern Gruening -
Carlos Borroto -
Ido Tamir -
Peter Cock