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Most recent version of code used on telescope with setVersion script and soft links for lib and src to the versions folder

This contains versions of the scalloping and no scalloping versions of the pfb. The version installed in this commit is the scalloping one. To install versions, use rsync -a and copy the appropriate directories (lib and src)  over.

Just updating everything. Change made to Makefile for cuda JIT issue. It's the first commented line of code.

Made changes to transpose and databuf.h. In transpose thread, I changed line 185 to ACQUIRE, and in flag_databuf.h, I changed VERBOSE to 1 and DEBUG to 1.

New New code

forgot to track the new beamform thread

Merging modified matlab files

Mid July/Aug Commissioning Improvements

This commit was made at the end of me leaving GBO during the middle of the July/Aug commissioning. Many of these updates have improved the performance of the pipeline. Performance measured in the frequency of stalled/hanging banks and bad blocks. We tuned core assignments, input block counts and more. Decreasesd the amount of time accessed by shared memory. Prevented packets sneaking through at the end of scans in the net thread. Removed the cpu transpose for the beamformer and implemented on the GPU.

Fixes to pfb corr mode. The GPU needed to flush the buffer that stores the last filter length worth of data. Also added new clean up logic lat waits until the net_thread has gone to the idle state. Also added a method for most threads that looks at the amount of locked blocks extending a hashpipe function

Updates from May commissioning

These commits contain the changes I made in the last few days at the May commissioning. I had gone through and made changes to hashpipe and the clean up structure for the threads. Before, hashpipe would temrinate the child process immediately, now the children terminate themselves and clean up then report to parent process. Also, hashpipe now clears shared memory and reclaims everything at the end and checks at the beginning. This commit also contains the fix to the PFB mode. The traspose thread to reduce data trasfered was indexing out of bounds.

Added while loops around semaphore-checking calls, which, for some reason, timeout instead of blocking until the semaphore is released...

Fixed the beamformer thread's cleanup issue in which a block with an earlier mcnt was accidentally processed

packet gen update for fx mode