FW: [quixote-qcdb] UPDATE Please run Lensfield
jens....@stfc.ac.uk
I checked out the code with:
hg clone http://bitbucket.org/petermr/lensfieldjumbo
and then unzipped the:
lensfield-0.1.1.zip
file therein and put the bin directory in my path.
I needed to run dos2unix on the lf file in the bin directory (and make it executable) as it had windows linefeeds, which confused bash:
-bash: /c/ccg/share/software/quixote/lensfieldjumbo/lensfield2-0.1.1/bin/lf: /bin/sh^M: bad interpreter: No such file or directory
I then ran mvn test from the lensfieldjumbo directory and got:
mht@cselnx1:/c/ccg/share/software/quixote/lensfieldjumbo> mvn test
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.115s
[INFO] Finished at: Tue Oct 12 16:36:48 BST 2010
[INFO] Final Memory: 4M/152M
[INFO] ------------------------------------------------------------------------
[ERROR] The goal you specified requires a project to execute but there is no POM in this directory (/c/ccg/share/software/quixote/lensfieldjumbo). Please verify you invoked Maven from the correct directory. -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MissingProjectException
I then cd'd into examples/gau and ran:
jmht@cselnx1:/c/ccg/share/software/quixote/lensfieldjumbo/examples/gau> lf gaussianArchive2Cml.lf
Exception in thread "main" java.lang.NoClassDefFoundError: org/lensfield/launcher/boot/Bootstrap
Best wishes,
Jens
-----Original Message-----
From: quixot...@googlegroups.com on behalf of Peter Murray-Rust
Sent: Tue 12/10/2010 15:56
To: quixot...@googlegroups.com
Subject: [quixote-qcdb] UPDATE Please run Lensfield
PLEASE READ AND PLEASE RUN.
Instructions for running Lensfield to convert (a) Gaussian archive (b)
GAMESSUK punch are in:
http://quixote.wikispot.org/Running_Lensfield_JUMBO_Examples
Please try to run these even if you don't need the results or don't use
these codes. That way we will get debug info rapidly.
In principle should should now be able to convert all your files of this
sort into CML.
The next phase is uploading and downloading from RESTful web-servers.
We also need to:
* convert to RDF
* post dictionaries
* run a triplestore
If we can do these before Oct21 I'll be very happy. The following are
probably highly dependent on these:
* chemical substructure search
* planning how to interface this to Avogadro
P.
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Peter Murray-Rust
I have re-committed my JUMBO code updates (which might have caused a problem) but these look like lensfield problems. Thanks for your patience. It's almost inevitable at this stage the system will have deployment problems.
Please add notes to the wiki if you solve any problems of know that there are identifiable issues
jens....@stfc.ac.uk
rm -rf lensfield2-0.1.1
hg pull
hg update
When I cd to examples/gau/:
jmht@cselnx1:/c/ccg/share/software/quixote/lensfieldjumbo/examples/gau> lf gaussianArchive2Cml.lf
** ERROR: Unable to resolve dependency org.lensfield:org.lensfield:lensfield2-api:jar:0.1.1:compile:0.1.1
Try running with '--update'
The repository system is offline and the requested artifact is not locally available at /home/jmht/.m2/repository/org/lensfield/lensfield2-api/0.1.1/lensfield2-api-0.1.1.jar
org.lensfield:lensfield2-api:jar:0.1.1
from the specified remote repositories:
(none)
Weerapong, you said you'd resolved this by setting LF_HOME - what did you set it to?
Thanks,
Jens
P.
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Weerapong Phadungsukanan
You will need to do hg pull and update again for lensfield jumbo. Sam has just fixed repository missing problem.
Now do
> cd lensfieldjumbo/examples/gau
> /pathtoLensfield2/bin/lf --update
> /pathtoLensfield2/bin/lf gaussianArchive2Cml.lf
I have got error message due to a class missing for last. I think Peter might have removed a class by mistake.
W
Weerapong Phadungsukanan
Under Linux, you will need to export environment variable LF_HOME=pathtoLensfield2. pathtoLensfield2 is directory where you extracted the zip files. For me, I am using Windows so my pathtoLensfield2 is C:\bin\lensfield2-0.1.1 and I have to add this environment variable LF_HOME manually.
You will need to do hg pull and update again for lensfield jumbo. Sam has just fixed repository missing problem.
Now do
> cd lensfieldjumbo/examples/gau
> /pathtoLensfield2/bin/lf --update
> /pathtoLensfield2/bin/lf gaussianArchive2Cml.lf
Weerapong
Pablo Echenique
Sam Adams
Hi,
It sounds like LF_HOME may not be set correctly; you shouldn't need to
set it at all, but if you do decide to then it needs to point to the
directory created when you unzip lensfield2-0.1.1.zip.
I've just got lensfield running on a clean linux box (one that hasn't
ever seen lensfield2 before) using the following sequence of commands
(full output below):
hg clone http://bitbucket.org/petermr/lensfieldjumbo
cd lensfieldjumbo/
unzip lensfield-0.1.1.zip
dos2unix lensfield2-0.1.1/bin/lf
chmod u+x lensfield2-0.1.1/bin/lf
export JAVA_HOME=/usr/lib/jvm/java-6-sun
export PATH=$PATH:$HOME/lensfieldjumbo/lensfield2-0.1.1/bin
lf --update
cd examples/gau/
lf gaussianArchive2Cml.lf
If I were to set LF_HOME, I would do:
export LF_HOME=$HOME/lensfieldjumbo/lensfield2-0.1.1
Regards,
Sam
Full output:
sea36@daedal:~$ hg clone http://bitbucket.org/petermr/lensfieldjumbo
destination directory: lensfieldjumbo
requesting all changes
adding changesets
adding manifests
adding file changes
added 5 changesets with 39 changes to 37 files
updating working directory
25 files updated, 0 files merged, 0 files removed, 0 files unresolved
sea36@daedal:~$ cd lensfieldjumbo/
sea36@daedal:~/lensfieldjumbo$ unzip lensfield-0.1.1.zip
Archive: lensfield-0.1.1.zip
creating: lensfield2-0.1.1/
...
sea36@daedal:~/lensfieldjumbo$ dos2unix lensfield2-0.1.1/bin/lf
sea36@daedal:~/lensfieldjumbo$ chmod u+x lensfield2-0.1.1/bin/lf
sea36@daedal:~/lensfieldjumbo$ export JAVA_HOME=/usr/lib/jvm/java-6-sun
sea36@daedal:~/lensfieldjumbo$ export
PATH=$PATH:/home/sea36/lensfieldjumbo/lensfield2-0.1.1/bin
sea36@daedal:~/lensfieldjumbo$ lf --update
Updating lensfield...
Downloading:
https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2-api/0.1.1/lensfield2-api-0.1.1.jar
...
Update complete
sea36@daedal:~/lensfieldjumbo$ cd examples/gau/
sea36@daedal:~/lensfieldjumbo/examples/gau$ lf gaussianArchive2Cml.lf
Lensfield2 (0.1.1)
----------------------------------------
[INFO] Checking build steps
[INFO] Resolving build order
[DEBUG] - files
[DEBUG] - cml
[INFO] Resolving dependencies
[DEBUG] Resolving global dependencies
[DEBUG] Resolving dependencies for: cml
Downloading:
https://maven.ch.cam.ac.uk/m2repo/cml/jumbo-converters-compchem/0.3-SNAPSHOT/jumbo-converters-compchem-0.3-SNAPSHOT.jar
...
[INFO] Initialising workspace
[INFO] Previous build log not found
[INFO] Starting build log
[INFO] Processing source: files
[DEBUG] (files) adding a/a.gau
[DEBUG] (files) adding a/a1/C2H5.gau
[DEBUG] (files) adding b/nh2.gau
[INFO] Processing build step: cml
LOADING CLASS:
org.xmlcml.cml.converters.compchem.gaussian.GaussianArchive2CMLConverter
----------
[DEBUG] (cml) reading a/a.gau
**/*.cml <0>/<1>.cml {*=a, **=a/}
[DEBUG] (cml) writing a/a.cml
[DEBUG] (cml) reading a/a1/C2H5.gau
**/*.cml <0>/<1>.cml {*=C2H5, **=a/a1/}
[DEBUG] (cml) writing a/a1/C2H5.cml
[DEBUG] (cml) reading b/nh2.gau
**/*.cml <0>/<1>.cml {*=nh2, **=b/}
[DEBUG] (cml) writing b/nh2.cml
----------------------------------------
BUILD COMPLETE
sea36@daedal:~/lensfieldjumbo/examples/gau$
Pablo Echenique
unzip lensfield-0.1.1.zip
dos2unix lensfield2-0.1.1/bin/lf
chmod u+x lensfield2-0.1.1/bin/lf
export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home
export PATH=$PATH:$HOME/lensfieldjumbo/lensfield2-0.1.1/bin
lf --update
cd examples/gau/
lf gaussianArchive2Cml.lf
jens....@stfc.ac.uk
When I run "lf --update":
Updating lensfield...
Downloading: https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2-api/0.1.1/lensfield2-api-0.1.1.jar
and it hangs.
After what I saw when I tried running "gaussianArchive2Cml.lf" file, namely:
lf gaussianArchive2Cml.lf
** ERROR: Unable to resolve dependency org.lensfield:org.lensfield:lensfield2-api:jar:0.1.1:compile:0.1.1
Try running with '--update'
The repository system is offline and the requested artifact is not locally available at /home/jmht/.m2/repository/org/lensfield/lensfield2-api/0.1.1/lensfield2-api-0.1.1.jar
org.lensfield:lensfield2-api:jar:0.1.1
from the specified remote repositories:
(none)
I manually downloaded "lensfield2-api-0.1.1.jar" to:
/home/jmht/.m2/repository/org/lensfield/lensfield2-api/0.1.1/lensfield2-api-0.1.1.jar
I then ran lf --update again and it said:
Updating lensfield...
Downloading: https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
so I again manually downloaded lensfield2-0.1.1.pom into /home/jmht/.m2/repository/org/lensfield/lensfield2-api/0.1.1/
However, the same trick doesn't seem to have worked, as it still tries to download the pom file:
Updating lensfield...
Downloading: https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
Any suggestions?
Thanks,
Jens
-----Original Message-----
From: quixote-...@googlegroups.com on behalf of Pablo Echenique
Sent: Wed 13/10/2010 10:59
To: quixote-...@googlegroups.com
Subject: Re: [quixote-qcdb-dev] FW: [quixote-qcdb] UPDATE Please run Lensfield
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Sam Adams
Hi,
I'm not sure, but you may be able to give java your proxy settings... Try editing the lensfield2-0.1.1/bin/lf file, adding the following to the 'exec java' command at the end of the file:
-Dhttp.proxyHost=proxyhostURL -Dhttp.proxyPort=proxyPortNumber -Dhttp.proxyUser=someUserName-Dhttp.proxyPassword=somePasswordThese arguments need to go before the 'org.lensfield.launcher.boot.Bootstrap' class name.
Regards,
Sam
-- Unilever Centre for Molecular Science Informatics Cambridge University Chemical Laboratories Tel: 01223 763073 Lensfield Road email: se...@cam.ac.uk Cambridge CB2 1EW
Weerapong Phadungsukanan
If you are using proxy in order to connect to internet, your maven should not work when you compile any projects with maven at all. You will need to set your maven to use proxy. Here is the guide :
http://maven.apache.org/guides/mini/guide-proxies.html
This should solve your problem for running maven from command line but it will not solve problem for lensfieldjumbo. Sam suggest should solve this problem.
If not, try pulling and updating lensfieldjumbo again. You may not have the latest version. There must be 5 changeset in your local mercurial repository.
Weerapong
jens....@stfc.ac.uk
> Do you have similar problem when you run 'mvn install' on other projects
> from command line?
I don't - most other stuff - updating the repositories, wget etc - all work fine (although the environment variable http_proxy does need to be set).
> If you are using proxy in order to connect to internet, your maven should
> not work when you compile any projects with maven at all. You will need to
> set your maven to use proxy. Here is the guide :
> http://maven.apache.org/guides/mini/guide-proxies.html
> This should solve your problem for running maven from command line but it
> will not solve problem for lensfieldjumbo. Sam suggest should solve this
> problem.
> If not, try pulling and updating lensfieldjumbo again. You may not have the
> latest version. There must be 5 changeset in your local mercurial
> repository.
Thanks for that suggestion - I did as suggested and now maven can at least download stuff (I tested it with jumbo-converters).
I tried Sam's suggestion and then reran update (shell debugging turned on):
jmht@cselnx1:/c/ccg/share/software/quixote/lensfieldjumbo> lf --update
+ '[' -z /usr/lib64/jvm/jre ']'
+ '[' -z /c/ccg/share/software/quixote/lensfieldjumbo/lensfield2-0.1.1 ']'
+ exec /usr/lib64/jvm/jre/bin/java -classpath /c/ccg/share/software/quixote/lensfieldjumbo/lensfield2-0.1.1/boot/boot-0.1.1.jar -Dlensfield.home=/c/ccg/share/software/quixote/lensfieldjumbo/lensfield2-0.1.1 -Dhttp.proxyHost=http://wwwcache3.dl.ac.uk -Dhttp.proxyPort=8080 org.lensfield.launcher.boot.Bootstrap --update
Updating lensfield...
Downloading: https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
and again it hangs.
I tried using wget to download lensfield2-0.1.1.pom, but even that just hangs:
mht@cselnx1:/c/ccg/share/software/quixote/lensfieldjumbo> wget https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
--2010-10-13 17:41:07-- https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
Resolving maven.ch.cam.ac.uk... 131.111.120.215
Connecting to maven.ch.cam.ac.uk|131.111.120.215|:443...
If I try downloading it on an external machine (i.e. outside the firewall), I get:
jmht@eeepc:~$ wget https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
--2010-10-13 17:24:59-- https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
Resolving maven.ch.cam.ac.uk... 131.111.120.215
Connecting to maven.ch.cam.ac.uk|131.111.120.215|:443... connected.
ERROR: certificate common name `www-metaprint2d.ch.cam.ac.uk' doesn't match requested host name `maven.ch.cam.ac.uk'.
To connect to maven.ch.cam.ac.uk insecurely, use `--no-check-certificate'.
Could that be part of the problem?
Thanks,
Jens
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jens....@stfc.ac.uk
I've tried again to run lensfield, but am still being scuppered by proxy issues.
The previous problem that I was having below with wget was due to my having set an http proxy, but not one for https.
Setting the environment variables http_proxy and https_proxy now mean that I can use curl or wget (the latter with --no-check-certificate) to download:
https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
However, if I run lf --update with the latest version of the code, I get the following:
jmht@cselnx1:/c/ccg/share/software/quixote/lensfieldjumbo> lf --update
+ '[' -z /usr/lib64/jvm/jre ']'
+ '[' -z /c/ccg/share/software/quixote/lensfieldjumbo/lensfield2-0.1.1 ']'
+ exec /usr/lib64/jvm/jre/bin/java -classpath /c/ccg/share/software/quixote/lensfieldjumbo/lensfield2-0.1.1/boot/boot-0.1.1.jar -Dlensfield.home=/c/ccg/share/software/quixote/lensfieldjumbo/lensfield2-0.1.1 -Dhttp.proxyHost=http://wwwcache3.dl.ac.uk -Dhttp.proxyPort=8080 -Dhttps.proxyHost=http://wwwcache3.dl.ac.uk -Dhttps.proxyPort=8080 org.lensfield.launcher.boot.Bootstrap --update
Updating lensfield...
Downloading: https://maven.ch.cam.ac.uk/m2repo/org/lensfield/lensfield2/0.1.1/lensfield2-0.1.1.pom
As you can see, I've tried setting https.proxyHost and https.proxyPort within the lf script, but they don't seem to be honoured as it is still just hanging.