cluster:147
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cluster:147 [2016/03/24 11:16] hmeij07 |
cluster:147 [2017/05/24 14:32] hmeij07 |
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| ==== BLCR Checkpoint in OL3 ==== | ==== BLCR Checkpoint in OL3 ==== | ||
| - | * This page concerns SERIAL jobs only | + | * This page concerns SERIAL jobs only; SERIAL jobs can restart on any node |
| * Installation and what it does [[cluster: | * Installation and what it does [[cluster: | ||
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| Checkpointing is an expensive operation so do not checkpoint under 6 hours. For example, if your job runs for a month checkpoint once a day, if your job runs for a week checkpoint every 12 hours. From this point on I expect all users to checkpoint. Some software does this internally (Amber, Gaussian). For applications or home grown code you can use BLCR. (Too bad it does not work out of box within Openlava). | Checkpointing is an expensive operation so do not checkpoint under 6 hours. For example, if your job runs for a month checkpoint once a day, if your job runs for a week checkpoint every 12 hours. From this point on I expect all users to checkpoint. Some software does this internally (Amber, Gaussian). For applications or home grown code you can use BLCR. (Too bad it does not work out of box within Openlava). | ||
| - | You need to test out checkpointing before you rely on it. I've notice that some local code, when opening files for output, BLCR does not notice it. The code below has such an example (file fid.txt). Hopefully future versions of BLCR will fix this. Or maybe we shuold | + | You need to test out checkpointing before you rely on it. I've notice that some local code, when opening files for output, BLCR does not notice it. The code below has such an example (file fid.txt). Hopefully future versions of BLCR will fix this. Or maybe we should |
| BLCR, Berkely Lab Checkpoint and Restart, remembers file paths and process ids. The code stages the necessary STDOUT and STDERR files Openlava generates and invokes the relocation feature while ignore old process ids. If an application is large, and static, it is advisable to not save the application inside the checkpoint file. | BLCR, Berkely Lab Checkpoint and Restart, remembers file paths and process ids. The code stages the necessary STDOUT and STDERR files Openlava generates and invokes the relocation feature while ignore old process ids. If an application is large, and static, it is advisable to not save the application inside the checkpoint file. | ||
| - | At the bottom of this page is the current version of '' | + | At the bottom of this page is the current version of '' |
| * Here is an interactive simple sample run. | * Here is an interactive simple sample run. | ||
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| Connection to petaltail lost. | Connection to petaltail lost. | ||
| - | # that was not too clever, log back in, restart application in another directory | + | # ooops, |
| [hmeij@petaltail 187]$ cd .. | [hmeij@petaltail 187]$ cd .. | ||
| [hmeij@petaltail sanscratch]$ mkdir 188 | [hmeij@petaltail sanscratch]$ mkdir 188 | ||
| Line 98: | Line 98: | ||
| < | < | ||
| - | [hmeij@cottontail ~/ynam]$ bsub < blcr_wrapper | + | [hmeij@cottontail ~/ynam]$ bsub < blcr_wrapper_serial |
| </ | </ | ||
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| ==== Files v0.2 ==== | ==== Files v0.2 ==== | ||
| - | * '' | + | * '' |
| < | < | ||
| Line 169: | Line 169: | ||
| if [ $mods -ne 2 ]; then | if [ $mods -ne 2 ]; then | ||
| echo " | echo " | ||
| - | | + | |
| fi | fi | ||
| Line 187: | Line 187: | ||
| else | else | ||
| echo " | echo " | ||
| - | | + | |
| fi | fi | ||
| Line 207: | Line 207: | ||
| #if [ " | #if [ " | ||
| # echo " | # echo " | ||
| - | # exit | + | # kill $$ |
| #fi | #fi | ||
| scp $checkpoints/ | scp $checkpoints/ | ||
| Line 223: | Line 223: | ||
| else | else | ||
| echo " | echo " | ||
| - | | + | |
| fi | fi | ||
| Line 277: | Line 277: | ||
| </ | </ | ||
| + | |||
| + | |||
| + | ==== Matlab ==== | ||
| + | |||
| + | * https:// | ||
| + | |||
cluster/147.txt ยท Last modified: 2020/02/27 13:06 by hmeij07
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