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13:24:51
usha
@cracauer - could you let me know how to proceed building the docker image of cando with my system?
13:25:57
usha
i understand that we can write a .lisp program and use clisp to get the output... how do we do the same thing with clasp?
13:26:22
usha
could anybody send me an example of how to write a simple clasp program and get the output?
13:27:00
drmeister
Hello usha: I'm in France at the moment at a conference. I gave Martin everything I had for building every form of clasp.
13:27:29
drmeister
He's probably moving into our incubator space today and then should be looking at the build system to automate everything.
13:27:50
drmeister
You can write a .lisp program and use clasp to get the output just like with clisp.
13:29:20
drmeister
There are other, more sophisticated ways to write software in Common Lisp using the Slime development environment. But creating a .lisp file and loading it is the simplest way.
13:32:01
drmeister
Martin hasn't built a docker image yet - but he has all of the scripts that I put together integrating his suggestions. I think he's going to familiarize himself with them this week as he automates things.
13:40:14
usha
Thank you the test file that I had worked fine. I am getting familiarized with lisp so that I can help write the TI module as well as with tleap and cando comparison
13:58:57
drmeister
Maybe you could come to Temple soon for another visit - if you are tackling Lisp we can give you a strong push in the right direction.
14:01:03
drmeister
It is problematic to compare excluded atom lists - but pairwise nonbond terms are easy to compare.
14:14:25
shiho
It's ready for comparing tleap and cando topology files. I'm trying to read both and checking the results.
14:27:27
usha
Sure @drmeister I can make a temple visit... please let me know preferable weeks for the visit and I will schedule it accordingly
14:29:46
usha
if we can compare whether all the steps taken by tleap and cando are the same it would be great
17:26:29
cracauer
well, it is more like infrastructure work. Especially for sending chemical computation jobs to worker computers. But yes, I use Clasp for almost everything now.
17:29:20
cracauer
Oh and those pesky python and js packages that are needed for cl-jupyter. Why do they have 3 package managers each?
17:30:17
Shinmera
drmeister also hinted that you might be able to take a look at clasp's usocket backend, which is pretty broken at the moment.
17:32:17
Shinmera
Well, in this case broken to the point where server sockets don't work at all and lots of tests fail
17:32:18
cracauer
Trying to feed a contiguous build now so that usha and others can pick up a working tree with cl-jupyter and cando.
17:41:29
usha
@shiho - the topology.lisp is the one that has the save-amber-parm-format, that generates the parameter files right?
18:35:37
shiho
Now, I'm developing read-amber-parm-format which is topology file reader to compare tleap and cando.
19:29:01
usha
@Shiho, could you make the exponent e symbol to E like the tleap so that it is easy for me to compare - because diff command sees it as different
19:43:32
drmeister
The order of all of the terms can be different and still describe the same system.
19:45:31
usha
i am comparing /cando/src/lisp/leap/topology.lisp and /amber/AmberTools/src/leap/src/leap/utilio.c
19:46:33
drmeister
usha: In leap I think there is more intrinsic ordering of objects. Atoms, residues, molecules are kept in the order that they are loaded.
19:47:22
drmeister
Trusting intrinsic order can create some really nasty bugs - so I don't like it. In Cando I try to avoid intrinsic ordering of things as much as possible.
19:47:56
drmeister
If objects are to be ordered - then those object keep a sequence number and they are sorted before they are written out.
19:51:09
drmeister
The tricky part is the nonbond interaction - because they aren't stored as a pair list - it's much more efficient to represent nonbonded interactions using an excluded atom list - to store what interactions are not calculated.
19:51:39
drmeister
To compare nonbonds you need to convert that into the interactions that are calculated.