Friday, July 29, 2016

Internship Week 4

I have finished converting the NVE code into an NVT code. The major changes that had to be made were the order of the subfunctions and the contents of the “movea” and “moveb” subfunctions. I sent it to my mentor for revision and copied the revised file into both of the Yale clusters that I have access to-- Omega and Grace. The revised file rearranged some of my original subfunctions, added in some outputs, and adjusted the velocity to 0. I was having trouble compiling the code in both clusters; every time I issued the command I received an error message informing me that the compilation had been aborted. I worked with my mentor and we found that there were complications in using the “scp” command to copy the code into the clusters. We copied and pasted in manually, as well as copying source files, but we only did this in Omega as opposed to both Omega and Grace.
I read up about scripts and refreshed on the vi editor for about an hour. My mentor created some scripts and I copied them into Omega under a directory that I created named “Scripts”. He explained the scripts to me line by line and I ran certain parts of them according to my immediate goal. For example, I put a pound sign in front of the lines of entire script except the loop that created 16 files under my “scratch” folder. After the loop, the script issued commands to open and close 16 files, so I copied a source file named “input.txt” into the space between the commands so that it would be copied into the 16 files. After this was done, I put pound signs in front of these lines because their job had already been executed. I then removed them from the loop that created a file named “ignition2.tasks”. Next, I put the pound signs back and removed one from the line that specified parameters such as the requested amount of time, the memory, the queue, etc. Then, I submitted the job. There were two other jobs already running.
When I returned the next day, the job was complete. I experimented with some commands on the cluster and attempted to edit some of the code so that it would produce outputs in a file.

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