Re: Corra - Installation Questions
Daniel Macedo Lorenzini
I could not install Corra on my computer, but I found your
CorraStatistics.R very useful to process the results I am getting from
the OpenMS software (http://open-ms.sourceforge.net/news.php). Could
you please send me an example of a APML file so I can use it to adapt
your R script to my data?
Thanks,
Daniel
2010/2/10 Mi-Youn Brusniak <mbru...@systemsbiology.org>:
> Dear Finbarr,
>
>
>
> There are three things to mention regarding your questions.
>
> Ø (1) The installation guide refers to 'EMV' as a required R package. From
> what I can tell, this is no longer available. Is this still a requirement?
>
> I seems like you are using latest R (2.10 and higher). We also encountered
> the old package bioconductor issue and we addressed in Corra v2.0 (which is
> not officially released). I attached CorraStatistics.zip file from Corra
> v2.0 so you can replace the CorraStatistics directory with this. The updated
> R codes are independent from deprecated EMV bioconductor. We have updated
> installation guide for Corra v2.0.
>
> Ø (2) During the deployment process, I received a CPP error - see attached.
> Would you have any suspicions as to (a) why this might have occurred, and
> (b) whether this is likely to affect the system? Prior to installing Corra,
> I updated all the software packages on my machine to their latest versions
> in the Ubuntu repository.
>
> Based on your attached log file, your compiler doesn’t have generic
> algorithm library. The sort function is the file is using C++ standard
> library called <algorithm.h>.
>
> Please consult your compiler in your OS.
>
>
>
> I think I rejected your request on joining the group since you were not
> using your work email address and we had a few incident of users who self
> joined with unidentifiable email address (such as generic google.com email)
> and circulate junk emails to group. Since I know you are genuine user, I
> added you in the discussion group : -)
>
>
>
> Have a great day!
>
>
>
> Mi-Youn
>
>
>
> Mi-Youn Brusniak, Ph.D.
>
> Computational Biology
>
> Seattle Proteome Center
>
> mbru...@systemsbiology.org
>
> Tel: (206) 732-1327
>
>
>
> From: Finbarr Tarrant [mailto:finbarr...@gmail.com]
> Sent: Tuesday, February 09, 2010 3:30 PM
> To: mbru...@systemsbiology.org
> Cc: finbarr...@ucd.ie
> Subject: Corra - Installation Questions
>
>
>
> Hi Mi-Youn,
>
>
>
> I'm a PhD student in UCD, Ireland, and I'm interested in using Corra.
>
>
>
> I've just worked through the installation procedure on a Ubuntu machine, and
> the webapp is running. I haven't processed any data yet.
>
>
>
> If you have a few minutes, would you mind having a look at two issues I've
> encountered?
>
>
>
> (1) The installation guide refers to 'EMV' as a required R package. From
> what I can tell, this is no longer available. Is this still a requirement?
>
>
>
> (2) During the deployment process, I received a CPP error - see attached.
> Would you have any suspicions as to (a) why this might have occurred, and
> (b) whether this is likely to affect the system? Prior to installing Corra,
> I updated all the software packages on my machine to their latest versions
> in the Ubuntu repository.
>
>
>
> Please let me know if you would like additional details such as software
> version numbers.
>
>
>
> Thanks,
>
> Finbarr
>
> --
> You received this message because you are subscribed to the Google Groups
> "Corra" group.
> To post to this group, send email to co...@googlegroups.com.
> To unsubscribe from this group, send email to
> corra+un...@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/corra?hl=en.
>
--
Daniel Macedo Lorenzini
Pontifícia Universidade Católica do Rio Grande do Sul
Centro de Pesquisas em Biologia Molecular e Funcional.
Av. Ipiranga, 668, Tecnopuc, Prédio 92A
90619-900 - Porto Alegre, RS - Brasil
fones: +55 51 8506 2296
+55 51 33203629
skype: daniel.macedo.lorenzini
Mi-Youn Brusniak
You can find an example APML files (sample_alignment.apml,
sample_alignment_large.apml, sample_peak_lists.apml) along with APML schema
.xsd files and html documents in
http://sourceforge.net/projects/corra/files/
We are also at the beginning stage of evaluation OpenMS. After the
performance evaluation for our dataset, we will be considering to plug
OpenMS into Corra.
So if you write code for converting OpenMS output to APML, we would highly
appreciate if you could contribute the code for future Corra release.
We are looking forward to hearing from you.
All the best,
Mi-Youn
Mi-Youn Brusniak, Ph.D.
Computational Biology
Seattle Proteome Center
mbru...@systemsbiology.org
Tel: (206) 732-1327
tomas
i've tried following instructions in APMLUserGuide.doc (those are the
only ones i found with installation advice), but could not succeed in
installing it on my Linux-Ubuntu run machine (with java 1.6.0_0). I
attach error messages, hopefully you would have some sort of advice of
what am i doing wrong.
Thanks, tomas
../APML$ java –Xms1g –Xmx1g -classpath ./bin/apmlviewer.jar;./lib/
dom4j-1.6.1.jar;./lib/jcommon-1.0.6.jar;./lib/jfreechart-1.0.6.jar;./
lib/JRclient.jar;./lib/log4j-1.2.8.jar;./lib/xbean-2.3.0.jar;./lib/
forms-1.0.7.jar;./lib/jdom.jar;./lib/jpat2.2jar;./lib/jung-1.7.6.jar;./
lib/stax-api-1.0.1.jar;./lib/xercesImpl.jar;./bin/apmlviewer.jar;./bin/
apml.jar;./bin/apml_schema.jar
ch.apmlViewer.mainAPMLViewer.mainAPMLViewer
Exception in thread "main" java.lang.NoClassDefFoundError: –Xms1g
Caused by: java.lang.ClassNotFoundException: –Xms1g
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:319)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:264)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:332)
Could not find the main class: –Xms1g. Program will exit.
invalid file (bad magic number): Exec format error
bash: ./lib/jcommon-1.0.6.jar: Permission denied
bash: ./lib/jfreechart-1.0.6.jar: Permission denied
Failed to load Main-Class manifest attribute from
/home/tomas/Desktop/APML/lib/JRclient.jar
invalid file (bad magic number): Exec format error
invalid file (bad magic number): Exec format error
bash: ./lib/forms-1.0.7.jar: Permission denied
bash: ./lib/jdom.jar: Permission denied
bash: ./lib/jpat2.2jar: No such file or directory
Failed to load Main-Class manifest attribute from
/home/tomas/Desktop/APML/lib/jung-1.7.6.jar
invalid file (bad magic number): Exec format error
bash: ./lib/xercesImpl.jar: Permission denied
bash: ./bin/apmlviewer.jar: Permission denied
bash: ./bin/apml.jar: Permission denied
bash: ./bin/apml_schema.jar: Permission denied
../APML$ java -cp ./bin/apml.jar;./bin/apml_schema.jar;./lib/
xbean-2.3.0.jar;./lib/log4j-1.2.8.jar
org.systemsbiology.apmlparser.v2.APMLParserApp ./doc/APML/
sample_alignment.apml test_out.apml
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
where options include:
-d32 use a 32-bit data model if available
-d64 use a 64-bit data model if available
-client to select the "client" VM
-server to select the "server" VM
-cacao to select the "cacao" VM
-zero to select the "zero" VM
-hotspot is a synonym for the "client" VM [deprecated]
The default VM is client.
-cp <class search path of directories and zip/jar files>
-classpath <class search path of directories and zip/jar files>
A : separated list of directories, JAR archives,
and ZIP archives to search for class files.
-D<name>=<value>
set a system property
-verbose[:class|gc|jni]
enable verbose output
-version print product version and exit
-version:<value>
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -jre-no-restrict-search
include/exclude user private JREs in the version
search
-? -help print this help message
-X print help on non-standard options
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions with specified granularity
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions with specified granularity
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -
agentlib:hprof
see also, -agentlib:jdwp=help and -
agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see
java.lang.instrument
-splash:<imagepath>
show splash screen with specified image
See http://java.sun.com/javase/reference for more details.
bash: ./bin/apml_schema.jar: Permission denied
invalid file (bad magic number): Exec format error
invalid file (bad magic number): Exec format error
Mark Christiansen
Perhaps I can help you get past this error. The problem lies with the character you are using for your Xms/Xmx flags. It should be java -Xms1g -Xmx1g (and the rest...) not java –Xms1g –Xmx1g (...). Although these dash characters look similar, they are different.
I hope this helps,
Mark
--
tomas
thanks for the advice, it did puzzle me why the heap functions did not
work. I also noticed a dot was missing in one of the jar filenames,
but other problems still persist - it seems to do with jar file format
recognition, but not in all cases, which is puzzling.
../APML$ java -Xms1g -Xmx1g -classpath ./bin/apmlviewer.jar;./lib/
dom4j-1.6.1.jar;./lib/jcommon-1.0.6.jar;./lib/jfreechart-1.0.6.jar;./
lib/JRclient.jar;./lib/log4j-1.2.8.jar;./lib/xbean-2.3.0.jar;./lib/
forms-1.0.7.jar;./lib/jdom.jar;./lib/jpat2.2.jar;./lib/
jung-1.7.6.jar;./lib/stax-api-1.0.1.jar;./lib/xercesImpl.jar;./bin/
apmlviewer.jar;./bin/apml.jar;./bin/apml_schema.jar
ch.apmlViewer.mainAPMLViewer.mainAPMLViewer
Usage: java [-options] class [args...]
...
See http://java.sun.com/javase/reference for more details.
invalid file (bad magic number): Exec format error
bash: ./lib/jcommon-1.0.6.jar: Permission denied
bash: ./lib/jfreechart-1.0.6.jar: Permission denied
Failed to load Main-Class manifest attribute from
/home/tomas/Desktop/APML/lib/JRclient.jar
invalid file (bad magic number): Exec format error
invalid file (bad magic number): Exec format error
bash: ./lib/forms-1.0.7.jar: Permission denied
bash: ./lib/jdom.jar: Permission denied
bash: ./lib/jpat2.2.jar: Permission denied
Failed to load Main-Class manifest attribute from
/home/tomas/Desktop/APML/lib/jung-1.7.6.jar
invalid file (bad magic number): Exec format error
bash: ./lib/xercesImpl.jar: Permission denied
bash: ./bin/apmlviewer.jar: Permission denied
bash: ./bin/apml.jar: Permission denied
bash: ./bin/apml_schema.jar: Permission denied
On Feb 24, 12:44 am, Mark Christiansen
<mchristian...@systemsbiology.org> wrote:
> Hi Tomas,
>
> Perhaps I can help you get past this error. The problem lies with the
> character you are using for your Xms/Xmx flags. It should be java -Xms1g
> -Xmx1g (and the rest...) not java –Xms1g –Xmx1g (...). Although these dash
> characters look similar, they are different.
>
> I hope this helps,
>
> Mark
>
> > Seehttp://java.sun.com/javase/referencefor more details.
> > bash: ./bin/apml_schema.jar: Permission denied
> > invalid file (bad magic number): Exec format error
> > invalid file (bad magic number): Exec format error
>
> > --
> > You received this message because you are subscribed to the Google Groups
> > "Corra" group.
> > To post to this group, send email to co...@googlegroups.com.
> > To unsubscribe from this group, send email to
> > corra+un...@googlegroups.com <corra%2Bunsu...@googlegroups.com>.
Mark Christiansen
To unsubscribe from this group, send email to corra+un...@googlegroups.com.
tomas
I got APML going. The problem was that the source jar files had to be
put in quotes and separated by colon, not semicolon.
At the moment i'm trying to run CorraApp, but i encouter errors there
as well. I set up Tomcat6 and the localserver ran smoothly, the build
process of Corra also was succesfull (a few errors in ../CPP_LIBRARY/
GENERAL/MATH_TOOLS/CC/simple_math.cc , while 'sort' is undeclared, but
i don't think it plays a role here), but while trying to login to the
App, i get the java error:
exception
javax.servlet.ServletException: Error instantiating servlet class
org.systemsbiology.apps.corragui.server.servlet.LoginServlet
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
102)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
293)
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
849)
org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:583)
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:
454)
java.lang.Thread.run(Thread.java:636)
root cause
java.lang.NoClassDefFoundError: Could not initialize class
org.apache.log4j.LogManager
org.apache.log4j.Logger.getLogger(Logger.java:104)
org.systemsbiology.apps.corragui.server.servlet.BaseServlet.<clinit>(BaseServlet.java:
14)
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:
57)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:
45)
java.lang.reflect.Constructor.newInstance(Constructor.java:532)
java.lang.Class.newInstance0(Class.java:372)
java.lang.Class.newInstance(Class.java:325)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
102)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
293)
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
849)
org.apache.coyote.http11.Http11Protocol
$Http11ConnectionHandler.process(Http11Protocol.java:583)
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:
454)
java.lang.Thread.run(Thread.java:636)
I tried various ways working on this problem, but the error message
remains unchanged.
Mark Christiansen
First of all, the NoClassDefFoundError indicates that the log4j jar file is not on your classpath. Are you able to add the jar to remove this error?
Also, the javax.servlet.ServletException suggests to me that Tomcat can't find your web.xml file. If you run the "webapp_build" target with ant, it will run "webapp_copy_conf" and copy the web.xml file for you into the webapp directory. What version of Tomcat are you running?
Let me know if this helps!
-Mark
--
tomas
thanks for your replies.
I'm running tomcat6. web.xml file is placed in its directory ( /var/
lib/tomcat6/webapps/CorraApp/WEB-INF ) after building Corra, so there
seems to be no problem with that.
I tried setting the CLASSPATH variable to the log4j jar file, but it
made no difference - the error remains the same. Actually, i tried
manually deleting the jar file in question and in that case i would
get the error that log4j class can not be found while running Corra -
this shows that Corra application is in fact linked with the library.
I don't understand the cause of getLogger error, since
LogManager.class is placed in the log4j.jar file.
tomas
On Mar 3, 2:32 am, Mark Christiansen
<mchristian...@systemsbiology.org> wrote:
> Hi Tomas,
>
> First of all, the NoClassDefFoundError indicates that the log4j jar file is
> not on your classpath. Are you able to add the jar to remove this error?
>
> Also, the javax.servlet.ServletException suggests to me that Tomcat can't
> find your web.xml file. If you run the "webapp_build" target with ant, it
> will run "webapp_copy_conf" and copy the web.xml file for you into the
> webapp directory. What version of Tomcat are you running?
>
> Let me know if this helps!
>
> -Mark
>
> > corra+un...@googlegroups.com <corra%2Bunsu...@googlegroups.com>.
Mark Christiansen
Your libraries should be within the webapps/CorraApp/WEB-INF/lib directory. Please verify that this is the case. If they are not present, then your ant build to populate the webapps directory is not complete.
I hope this helps.
-Mark
To unsubscribe from this group, send email to corra+un...@googlegroups.com.
tomas
all of the libraries are indeed in the folder you mentioned (including
log4j-1.2.14.jar), ant build was successful. That's what i tried to
say in my last post - if i delete the log4j-1.2.14.jar manually, the
get error in Corra that the following library class be found - this
points that the associations of Corra with libraries are fine. There
seems to be an error within log4j class package itself.
tomas
On Mar 13, 11:41 pm, Mark Christiansen
<mchristian...@systemsbiology.org> wrote:
> Hi Tomas,
>
> Your libraries should be within the webapps/CorraApp/WEB-INF/lib directory.
> Please verify that this is the case. If they are not present, then your
> ant build to populate the webapps directory is not complete.
>
> I hope this helps.
>
> -Mark
>
> > corra%2Bunsu...@googlegroups.com<corra%252Buns...@googlegroups.com>
Mark Christiansen
I believe your tomcat is not installed properly. Are you running it on Windows or Linux? Do you have an environment variable CATALINA_HOME set to your tomcat directory? Also, do you have another environment variable JAVA_HOME pointing to your JDK directory? These are requirements that tomcat has in order to serve your servlets properly. Also, in your PATH you should add your JDK's bin directory.
I hope this helps,
Mark
To unsubscribe from this group, send email to corra+un...@googlegroups.com.
tomas
you were right - my Tomcat version (automatically installed from
ubuntu repositories) was faulty. I thought that it was okay, because
example jsp/servlet files i tried out worked fine, but when i tried
running Corra on another Tomcat version (apache-tomcat-6.0.26), i
could finally login to Corra.
The program itself still doesn't function normally though. No
information pops-up when clicking "About corra", "References" etc,
analysis itself run unsuccessfully as well, which must have to do with
faulty building of Corra (sh deploy_corra.sh).
There were many errors regarding missing includes in corra's library
*.c and *.h files (they were missing either include <algorithm>,
either <iostream>, either <cstring> amongst others). This error i
don't know ho to fix though:
../../CPP_LIBRARY/RATIOLIZER/CC/protein_ratiolizer.cc: In member
function ‘void
protein_ratiolizer::print_protein_analysis(PROTEIN_RATIO*)’:
../../CPP_LIBRARY/RATIOLIZER/CC/protein_ratiolizer.cc:372: error: no
matching function for call to
‘find(__gnu_cxx::__normal_iterator<std::pair<double, PEPTIDE_RATIO*>*,
std::vector<std::pair<double, PEPTIDE_RATIO*>,
std::allocator<std::pair<double, PEPTIDE_RATIO*> > > >,
__gnu_cxx::__normal_iterator<std::pair<double, PEPTIDE_RATIO*>*,
std::vector<std::pair<double, PEPTIDE_RATIO*>,
std::allocator<std::pair<double, PEPTIDE_RATIO*> > > >,
std::pair<double, PEPTIDE_RATIO*>&)’
make: *** [../obj/protein_ratiolizer.o] Error 1
p.s. I'm using Ubuntu Linux distribution.
Hope you know how to get over this.. I still expect many other errors
to follow latter though.
Thanks,
tomas
On Mar 15, 11:38 pm, Mark Christiansen
<mchristian...@systemsbiology.org> wrote:
> Hi Tomas,
>
> Windows or Linux? Do you have an environment variable CATALINA_HOME set to
> your tomcat directory? Also, do you have another environment variable
> JAVA_HOME pointing to your JDK directory? These are requirements that
> tomcat has in order to serve your servlets properly. Also, in your PATH you
> should add your JDK's bin directory.
>
> I hope this helps,
>
> Mark
>
Mark Christiansen
I am glad you made progress configuring Corra. Unfortunately, "About corra" and "references" are currently incomplete. So your installation is working properly here.
The first thing I think you should look into is building SuperHirn. You may need to download it here: http://prottools.ethz.ch/muellelu//web/SuperHirn/code/SuperHirn.0.03.zip
Extract these files as expected by deploy_corra.sh. You will need to rename the folder from SuperHirnv3 to SuperHirn. Then change to the make directory ($CORRA_DIR/SuperHirn/SuperHirn/make) and see if you can make SuperHirn manually with the "make" command.
If you are still unable to successfully compile SuperHirn, I suggest checking which shell you use and the version of gcc. I am running tcsh and gcc v4.1.2 and am able to build SuperHirn.
Please let me know if this information helps and if you need any future assistance!
-Mark
tomas
thanks for your links.
The program finally builds successfully (there are quite a few
warnings while making, though). Still some includes had to be added to
the library - i can't imagine program building on your PC otherwise
(i'm running gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9)).
Analysis of the example mzXML files i tried still fails. Maybe you
could share some example mzXML file, Mark? Would be really
appreciated.
From corra_jobmanager.log (after running feature picking):
Apr 28, 11:26:03 AM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 23]
(ExecutorManager.java:137) - removing failed executors : 1
Apr 28, 11:26:03 AM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 23]
(ExecutorManager.java:143) - After removing failed executors -- Total
executors: 0
tomas
On Apr 19, 11:28 pm, Mark Christiansen
<mchristian...@systemsbiology.org> wrote:
> Hi Tomas,
>
> > <corra%252Buns...@googlegroups.com<corra%25252Bun...@googlegroups.com>
Mark Christiansen
I have not had to add any includes to the library to build successfully. However, it would be nice to incorporate your findings for other users. Could you tell me which includes you had to add?
Please download the following file I have set up for you: ftp://ftp.systemsbiology.org/Corra/example_mzXML.tgz This will have examples of mzXML files. Let me know how else I can help!
Cheers,
Mark
tomas
the additions i had to make to the library you posted, in order to
build successfully (they had to be made because the c library was
requested by either of printf, sort, strlen, strcmp functions):
#include <cstdio> added to
GENERAL/CC/progress_bar.cc
PEAK_DETECTION/FT/MSProcessing/CC/CentroidPeak.cpp
#include <cstring> added to
GENERAL/CC/data_plotter.cc
GENERAL/CC/feature.cc
GENERAL/CC/ms2_info.cc
GENERAL/CC/LC_MS_XML_writer.cc
GENERAL/CC/LC_MS_APML_writer.cc
GENERAL/CC/file_reader.cc
GENERAL/CC/file_sys.cc
GENERAL/CC/EM_fitter.cc
GENERAL/CC/read_param.cc
#include <iostream> added to
PEAK_DETECTION/FT/MS1Level/include/Deisotoper.h
Thanks for uploading the example. Sadly i hadn't had the opportunity
to try it out properly yet, since after updating my ubuntu system, the
Corra application messed up again :/ I think it has to do with sun-
java6-jdk being replaced by openjdk in the latest edition of ubuntu, i
haven't had the time to find out the cause yet. I will let you know
how it all goes.
Greetings,
tomas
On Apr 28, 11:44 pm, Mark Christiansen
<mchristian...@systemsbiology.org> wrote:
> Hi Tomas,
>
> However, it would be nice to incorporate your findings for other users.
> Could you tell me which includes you had to add?
>
> Please download the following file I have set up for you:ftp://ftp.systemsbiology.org/Corra/example_mzXML.tgz This will have
> examples of mzXML files. Let me know how else I can help!
>
> Cheers,
>
> Mark
>
>
> read more »
Mark Christiansen
Thanks for the information. I will see if future releases can include the changes you pointed out.
By the way, we have not attempted an Ubuntu install before, but I believe the problems you are having can be resolved easily by changing back to the JDK with the following command:
I hope this helps,
Mark
tomas
well i simply installed an older version of ubuntu on my partition,
works fine there :D
Or at least from the first sight - i still think there's something
wrong with the performing of java functions while running the program,
because feature picking fails with the sample files you provided me
with. This is the output of my corra_jobmanager.log file:
May 31, 2:27:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:86) - Idle......
May 31, 2:27:22 PM DEBUG [http-8080-5] (ExecutorManager.java:53) -
Adding executor -- SpecArray_feature_picking
May 31, 2:27:22 PM DEBUG [http-8080-5] (ExecutorManager.java:55) -
Number of executors in queue: 1
May 31, 2:27:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:103) - Start Pending executors....
May 31, 2:27:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:125) - adding executor to toExecute
May 31, 2:27:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:130) - After starting executors -- Running
executors: 1; Total executors: 1
May 31, 2:27:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:137) - removing failed executors : 0
May 31, 2:28:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:103) - Start Pending executors....
May 31, 2:28:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:130) - After starting executors -- Running
executors: 1; Total executors: 1
May 31, 2:28:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:137) - removing failed executors : 0
May 31, 2:29:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:103) - Start Pending executors....
May 31, 2:29:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:130) - After starting executors -- Running
executors: 1; Total executors: 1
May 31, 2:29:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:137) - removing failed executors : 0
May 31, 2:30:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:103) - Start Pending executors....
May 31, 2:30:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:130) - After starting executors -- Running
executors: 1; Total executors: 1
May 31, 2:30:22 PM DEBUG
[org.systemsbiology.apps.corragui.server.executor.ExecutorManager 22]
(ExecutorManager.java:137) - removing failed executors : 0
May 31, 2:30:32 PM DEBUG [Thread-14] (ExecutorManager.java:173) -
After executor failed -- Running executors: 0; Total executors: 0
As far as i understand, feature picking fails to start properly. Maybe
you have any other clues what clues may i look for to find the root of
the problem?
Greetings,
tomas
On May 11, 12:54 am, Mark Christiansen
<mchristian...@systemsbiology.org> wrote:
> Hi Tomas,
>
> changes you pointed out.
>
> By the way, we have not attempted an Ubuntu install before, but I believe
> the problems you are having can be resolved easily by changing back to the
> JDK with the following command:
>
> sudo update-alternatives --config java
>
> I hope this helps,
>
> Mark
>
>
> read more »
Mark Christiansen
It seems that the executors are getting added to the queue as is required. The next step is to verify that the installation of your batch management system works properly. Are you using PBS, LSF, or another system?
The easiest way to troubleshoot your setup is to find the deployed "users" directory on your system. Once you find it, you will see a subdirectory for the user you made in Corra. Under this should be the project you ran the executors on. If you are using PBS, you will see a PBS directory populated with shell scripts. Run the shell script from its directory by issuing "qsub <shellscript>.sh". The script should finish without any errors if PBS is configured properly.
Please let me know what you find out and if you have any further questions.
Regards,
Mark
> ...
>
> read more »
tomas
my project folder indeed contains PBS with a shell script inside. But
when i try to run the command you pasted, i am asked to install either
gridengine-client or torque-client. As far as i understand, the
packages handle cluster computing, and neither of them was pasted in
the Corra-installation guide under the requirements. Gridengine
requires some non-trivial set up, while torque-client requires some
torqueserver being deployed, if i'm not mistaken.
I won't be able run Corra without deploying one of these programs
though, right?
tomas
On May 31, 9:13 pm, Mark Christiansen
> Hello Tomas,
>
> It seems that the executors are getting added to the queue as is required.
> The next step is to verify that the installation of your batch management
> system works properly. Are you using PBS, LSF, or another system?
>
> The easiest way to troubleshoot your setup is to find the deployed "users"
> directory on your system. Once you find it, you will see a subdirectory for
> the user you made in Corra. Under this should be the project you ran the
> executors on. If you are using PBS, you will see a PBS directory populated
> with shell scripts. Run the shell script from its directory by issuing
> "qsub <shellscript>.sh". The script should finish without any errors if PBS
> is configured properly.
>
> Please let me know what you find out and if you have any further questions.
>
> Regards,
>
> Mark
>
>
> read more »
Pieter Neerincx
Just to chime in. I'm trying to setup a Corra server too and I think I have the same problem. The list of dependencies does not mention PBS (or Gridengine) and since I'm just trying to create a test-server without cluster as a backend, I assumed I could forget about PBS. But from what I see in the logs it appears that installation of PBS is required even if you simply want to run the jobs on the same machine... Right?
Cheers,
Pi
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Mi-Youn Brusniak
Yes. you are right. Since Corra has a purpose to processing in high through put of many LC-MS run and to get more statistical confidence on detection of differentially expressed features that can be a biomarker to do follow up study, we deliberately designed Corra architecture to work with distributed system such as PBS or LFS or others if users want to plug-in theirs.
Thus, Corra is not the desktop application for running a few LC-MS runs.
However, due to some requests from small academic labs, we are thinking about adding a module to deal with single CPU (though it's probably not desirable for high throughput > 50 LC-MS etc).
We will keep you updated.
Cheers,
Mi-Youn