Dear all,
I tried to install IMP today in our cluster and I ran into a small problem with MODELLER. IMP could not find MODELLER, despite the directory and all the paths being perfectly fine. I double checked the modeller_test.py in scons_test/ and I found that the regular expression looking for mod9v10 instead of mod9.10. After changing the expression all went well. Maybe this changed with the last version of MODELLER.
Just letting you know for future reference!
An additional question, should I use the version 1.0 or the SVN?
Cheers,
João [...] Rodrigues http://nmr.chem.uu.nl/~joao
On 10/20/11 9:44 AM, João Rodrigues wrote: > I tried to install IMP today in our cluster and I ran into a small > problem with MODELLER. IMP could not find MODELLER, despite the > directory and all the paths being perfectly fine. I double checked the > modeller_test.py in scons_test/ and I found that the regular expression > looking for mod9v10 instead of mod9.10. After changing the expression > all went well. Maybe this changed with the last version of MODELLER.
Yes, since IMP 1.0 was released before newer versions of MODELLER, it cannot correctly detect them. The MODELLER test was changed in IMP SVN some time ago so that it works correctly.
> An additional question, should I use the version 1.0 or the SVN?
There are many new features in SVN, so it's probably a better choice than 1.0. However, it is under active development, so you may occasionally run into problems building the code; check the nightly build status page at http://salilab.org/imp/nightly/tests.html to see if the modules you want to use are working.
Ben
Hey Ben,
Thanks for the quick answer. I'm indeed running into some problems compiling/building IMP. The 1.0 version fails because of some library dependencies I can't solve, but that's not IMP, it's our cluster setup.... The SVN version fails because of a KeyError:
Building tools/imppy.sh scons: *** [tools/imppy.sh] KeyError : 'kernel' Traceback (most recent call last): File "/home/software/software/scons/scons-2.1.0/..//lib/scons-2.1.0/SCons/Action.py", line 1062, in execute File "/home/software/software/IMP/src/scons_tools/imppy.py", line 61, in builder_script_file if data.get(env).modules['kernel'].external: KeyError: 'kernel' scons: building terminated because of errors.
What do you reckon of this?
Best,
João
On 10/20/11 10:15 AM, João Rodrigues wrote: > Thanks for the quick answer. I'm indeed running into some problems > compiling/building IMP. The 1.0 version fails because of some library > dependencies I can't solve, but that's not IMP, it's our cluster > setup.... The SVN version fails because of a KeyError: > > Building tools/imppy.sh > scons: *** [tools/imppy.sh] KeyError : 'kernel' > Traceback (most recent call last): > File > "/home/software/software/scons/scons-2.1.0/..//lib/scons-2.1.0/SCons/Action.py", > line 1062, in execute > File "/home/software/software/IMP/src/scons_tools/imppy.py", line > 61, in builder_script_file > if data.get(env).modules['kernel'].external: > KeyError: 'kernel' > scons: building terminated because of errors.
That's odd - is this a fresh checkout? Did the kernel module configure correctly (you should see that further up in the scons output) ? If not, that would be a concern, since pretty much everything requires the kernel module, so you won't get far without it.
Ben
That error tends to mean you are doing an out of source build, but forgot a "repository='something'" line in your config.py (or don't have a config.py at all).
On Fri, Oct 21, 2011 at 3:31 PM, Ben Webb ben@salilab.org wrote:
> On 10/20/11 10:15 AM, João Rodrigues wrote: > > Thanks for the quick answer. I'm indeed running into some problems > > compiling/building IMP. The 1.0 version fails because of some library > > dependencies I can't solve, but that's not IMP, it's our cluster > > setup.... The SVN version fails because of a KeyError: > > > > Building tools/imppy.sh > > scons: *** [tools/imppy.sh] KeyError : 'kernel' > > Traceback (most recent call last): > > File > > > "/home/software/software/scons/scons-2.1.0/..//lib/scons-2.1.0/SCons/Action.py", > > line 1062, in execute > > File "/home/software/software/IMP/src/scons_tools/imppy.py", line > > 61, in builder_script_file > > if data.get(env).modules['kernel'].external: > > KeyError: 'kernel' > > scons: building terminated because of errors. > > That's odd - is this a fresh checkout? Did the kernel module configure > correctly (you should see that further up in the scons output) ? If not, > that would be a concern, since pretty much everything requires the > kernel module, so you won't get far without it. > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >
And, yes, we should probably make sure that it produces something a littler nicer :-)
On Sun, Oct 23, 2011 at 8:31 AM, Daniel Russel drussel@gmail.com wrote:
> That error tends to mean you are doing an out of source build, but forgot a > "repository='something'" line in your config.py (or don't have a config.py > at all). > > > On Fri, Oct 21, 2011 at 3:31 PM, Ben Webb ben@salilab.org wrote: > >> On 10/20/11 10:15 AM, João Rodrigues wrote: >> > Thanks for the quick answer. I'm indeed running into some problems >> > compiling/building IMP. The 1.0 version fails because of some library >> > dependencies I can't solve, but that's not IMP, it's our cluster >> > setup.... The SVN version fails because of a KeyError: >> > >> > Building tools/imppy.sh >> > scons: *** [tools/imppy.sh] KeyError : 'kernel' >> > Traceback (most recent call last): >> > File >> > >> "/home/software/software/scons/scons-2.1.0/..//lib/scons-2.1.0/SCons/Action.py", >> > line 1062, in execute >> > File "/home/software/software/IMP/src/scons_tools/imppy.py", line >> > 61, in builder_script_file >> > if data.get(env).modules['kernel'].external: >> > KeyError: 'kernel' >> > scons: building terminated because of errors. >> >> That's odd - is this a fresh checkout? Did the kernel module configure >> correctly (you should see that further up in the scons output) ? If not, >> that would be a concern, since pretty much everything requires the >> kernel module, so you won't get far without it. >> >> Ben >> -- >> ben@salilab.org http://salilab.org/~ben/ >> "It is a capital mistake to theorize before one has data." >> - Sir Arthur Conan Doyle >> _______________________________________________ >> IMP-users mailing list >> IMP-users@salilab.org >> https://salilab.org/mailman/listinfo/imp-users >> > >
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Ben Webb -
Daniel Russel -
João Rodrigues