Domain specific discussions: Computational chemistry, molecular dynamics, bioinformatics, etc. Surajit Bhattacharya https://tis.xsede.org/c/message_boards/find_message?p_l_id=&messageId=2048926 2019-01-06T02:31:08Z 2019-01-06T02:31:08Z

Hi,<br /><br />I am new to xsede. We are trying to reassemble a human genome using canu. But the major problem to run it is its memory and time requirements. the particular tool is divided into multiple modules and each module requires 64-512GB memory to run (based on the module requirements). Also the time for a minimum run for a human assembly is approx &gt;20 days. We have been allocated TACC stampede2 server. If any one has run canu on stampede or any other tool which has similar issues, can guide us regarding running such tools that would help us immensely.<br /><br />Please let me know if you would have any other question regarding the same.<br /><br />Surajit

Surajit Bhattacharya 2019-01-06T02:31:08Z Charity Lovitt https://tis.xsede.org/c/message_boards/find_message?p_l_id=&messageId=656222 2014-01-31T20:46:55Z 2014-01-31T20:46:55Z

I am a frequent user of XSEDE and gaussian (Trestles). <br /><br />When I started with XSEDE, I borrowed a script from a colleague of mine from Germany. However, the script is too complex for me to understand and modify, especially when machines are updated. <br /><br />I know that there are many other gaussian users in XSEDE so I ask this question. How do you submit jobs to the queue? Would you be willing to share scripts with other users? <br /><br />Currently, I&#039;m trying to run jobs on Trestles but I will need to run Gamess on other systems. <br /><br />I look forward to the conversation!<br /><br />Charity

Charity Lovitt 2014-01-31T20:46:55Z