|
1 | 1 | --- |
2 | | -title: "Troubleshooting" |
| 2 | +title: "Frequently asked questions" |
3 | 3 | output: |
4 | 4 | rmarkdown::html_vignette |
5 | 5 | vignette: > |
6 | | - %\VignetteIndexEntry{Troubleshooting} |
| 6 | + %\VignetteIndexEntry{FAQ} |
7 | 7 | %\VignetteEngine{knitr::rmarkdown} |
8 | 8 | %\VignetteEncoding{UTF-8} |
9 | 9 | --- |
@@ -58,59 +58,6 @@ compiler installed that you need to add to your `$PATH` or load as a module. |
58 | 58 | Once this is set, you can install the package from R *that was started in a |
59 | 59 | terminal that has this module/path active*. |
60 | 60 |
|
61 | | -## Job submission fails with template error {#template} |
62 | | - |
63 | | -If you test your setup with a simple `Q` call, but get an error like the |
64 | | -following: |
65 | | - |
66 | | -```{r eval=FALSE} |
67 | | -> clustermq::Q(identity, x=1, n_jobs=1) |
68 | | -Submitting 1 worker jobs (ID: cmq6053) ... |
69 | | -Unable to run job: unknown resource "m_mem_free" |
70 | | -Exiting. |
71 | | -
|
72 | | -The filled SGE template ‘~/R/x86_64-pc-linux-gnu-library/4.2/clustermq/SGE.tmpl’ was: |
73 | | -""" |
74 | | -#$ -N cmq6053 |
75 | | -#$ -j y |
76 | | -#$ -o /dev/null |
77 | | -#$ -cwd |
78 | | -#$ -V |
79 | | -#$ -t 1-1 |
80 | | -#$ -pe smp 1 |
81 | | -#$ -l m_mem_free=1073741824 |
82 | | -
|
83 | | -ulimit -v $(( 1024 * 4096 )) |
84 | | -CMQ_AUTH=xxxx R --no-save --no-restore -e 'clustermq:::worker("tcp://10.0.0.100:6053")' |
85 | | -""" |
86 | | -
|
87 | | -see: https://mschubert.github.io/clustermq/articles/troubleshooting.html#template |
88 | | -
|
89 | | -Error in initialize(...) : Job submission failed with error code 1 |
90 | | -In addition: Warning message: |
91 | | -In system2("qsub", input = filled, stdout = TRUE) : |
92 | | - running command ''qsub' < '/tmp/RtmpdGJOxs/filee7f3011007b'' had status 1 |
93 | | -``` |
94 | | - |
95 | | -This means that your job submission system has not been successfully |
96 | | -auto-detected and requires some configuration, _i.e._ you need to manually |
97 | | -specify what scheduler and template you want to use. |
98 | | - |
99 | | -Be sure to know which scheduler your HPC provides, and then see the [manual |
100 | | -scheduler setup](https://mschubert.github.io/clustermq/articles/userguide.html#scheduler-templates) |
101 | | -on how to set it up. |
102 | | - |
103 | | -You may need to change some scheduler-specific options in the template file for |
104 | | -this to work, like the queue/partition name or how to request memory or |
105 | | -runtime. Often, the error message gives you a good hint on what to change: In |
106 | | -the example above, we are using a version of SGE where we need to use |
107 | | -`mem_free` instead of `m_mem_free` to request memory. |
108 | | - |
109 | | -If it is not obvious what do change, consult the scheduler documentation or |
110 | | -your system admins for more information. For the latter, provide them with the |
111 | | -filled template from the error message (as this is an HPC submission template |
112 | | -issue rather than a `clustermq` package issue). |
113 | | - |
114 | 61 | ## Session gets stuck at "Running calculations" {#stuck} |
115 | 62 |
|
116 | 63 | Your R session may be stuck at something like the following: |
|
0 commit comments