| Both sides previous revision
Previous revision
|
Next revision
Both sides next revision
|
grid [2017/09/27 18:56]
popel |
grid [2017/09/27 19:10]
popel |
| * For interactive work, you can use ''qrsh'', but please try to end the job (exit with Ctrl+D) once finished with your work, especially if you ask for a lot of memory or CPUs (see below). One semi-permanent qrsh job (with non-extreme CPU/mem requirements) per user is acceptable. | * For interactive work, you can use ''qrsh'', but please try to end the job (exit with Ctrl+D) once finished with your work, especially if you ask for a lot of memory or CPUs (see below). One semi-permanent qrsh job (with non-extreme CPU/mem requirements) per user is acceptable. |
| * **Specify the memory and CPU requirements** (if higher than the defaults) and **don't exceed them**. | * **Specify the memory and CPU requirements** (if higher than the defaults) and **don't exceed them**. |
| * If your job needs more than one CPU (on a single machine) for most of the time, reserve the given number of CPU cores (and SGE slots) with <code>qsub -pe smp <number-of-CPU-cores></code> (As you can see in [[#List of Machines]], the maximum is 32 cores). If your job needs e.g. up to 110% CPU most of the time and just occasionally 200%, it is OK to reserve just one core (so you don't waste). | * If your job needs more than one CPU (on a single machine) for most of the time, reserve the given number of CPU cores (and SGE slots) with <code>qsub -pe smp <number-of-CPU-cores></code> As you can see in [[#List of Machines]], the maximum is 32 cores. If your job needs e.g. up to 110% CPU most of the time and just occasionally 200%, it is OK to reserve just one core (so you don't waste). TODO: when using ''-pe smp -l mf=8G,amf=8G,h_vmem=12G'', which memory limits are per machine and which are per core? |
| * If you are sure your job needs less than 1GB RAM, then you can skip this. Otherwise, if you need e.g. 8 GiB, you must always use ''qsub'' (or ''qrsh'') with ''-l mem_free=8G''. You should specify also ''act_mem_free'' with the same value and ''h_vmem'' with possibly a slightly bigger value. See [[#memory]] for details. TL;DR: <code>qsub -l mem_free=8G,act_mem_free=8G,h_vmem=12G</code> | * If you are sure your job needs less than 1GB RAM, then you can skip this. Otherwise, if you need e.g. 8 GiB, you must always use ''qsub'' (or ''qrsh'') with ''-l mem_free=8G''. You should specify also ''act_mem_free'' with the same value and ''h_vmem'' with possibly a slightly bigger value. See [[#memory]] for details. TL;DR: <code>qsub -l mem_free=8G,act_mem_free=8G,h_vmem=12G</code> |
| * Be kind to your colleagues. If you are going to submit jobs that effectively occupy more than one fifth of our cluster for more than several hours, check if the cluster is free (with ''qstat -g c'' or ''qstat -u \*'') and/or ask your colleagues if they don't plan to use the cluster intensively in the near future. Note that if you allocate one slot (CPU core) on a machine, but (almost) all its RAM, you have effectively occupied the whole machine and all its cores. | * Be kind to your colleagues. If you are going to submit jobs that effectively occupy more than one fifth of our cluster for more than several hours, check if the cluster is free (with ''qstat -g c'' or ''qstat -u \*'') and/or ask your colleagues if they don't plan to use the cluster intensively in the near future. Note that if you allocate one slot (CPU core) on a machine, but (almost) all its RAM, you have effectively occupied the whole machine and all its cores. |
| * **act_mem_free** (or amf) is a ÚFAL-specific option, which specifies the real amount of free memory (at the time of scheduling). You can specify it when submitting a job and it will be scheduled to a machine with at least this amount of memory free. In an ideal world, where no jobs are exceeding their ''mem_free'' requirements, we would not need this options. However, in real world it is recommended to use this option with the same value as ''mem_free'' to protect your job from failing with out-of-memory error (because of naughty jobs of other users). | * **act_mem_free** (or amf) is a ÚFAL-specific option, which specifies the real amount of free memory (at the time of scheduling). You can specify it when submitting a job and it will be scheduled to a machine with at least this amount of memory free. In an ideal world, where no jobs are exceeding their ''mem_free'' requirements, we would not need this options. However, in real world it is recommended to use this option with the same value as ''mem_free'' to protect your job from failing with out-of-memory error (because of naughty jobs of other users). |
| * **h_vmem** is equivalent to setting ''ulimit -v'', i.e. it is a hard limit on the size of virtual memory (see RLIMIT_AS in ''man setrlimit''). If your job exceeds this limit, memory allocation fails (i.e., malloc or mmap will return NULL), and your job will probably crash on SIGSEGV. TODO: according to ''man queue_conf'', the job is killed with SIGKILL, not with SIGSEGV. Note that ''h_vmem'' specifies the maximal size of **allocated_memory, not used_memory**, in other words it is the VIRT column in ''top'', not the RES column. SGE does not use this parameter in any other way. Notably, job scheduling is not affected by this parameter and therefore there is no guarantee that there will be this amount of memory on the chosen machine. The problem is that some programs (e.g. Java with the default setting) allocate much more (virtual) memory than they actually use in the end. If we want to be ultra conservative, we should set ''h_vmem'' to the same value as ''mem_free''. If we want to be only moderately conservative, we should specify something like h_vmem=1.5*mem_free, because some jobs will not use the whole mem_free requested, but still our job will be killed if it allocated much more than declared. The default effectively means that your job has no limits. | * **h_vmem** is equivalent to setting ''ulimit -v'', i.e. it is a hard limit on the size of virtual memory (see RLIMIT_AS in ''man setrlimit''). If your job exceeds this limit, memory allocation fails (i.e., malloc or mmap will return NULL), and your job will probably crash on SIGSEGV. TODO: according to ''man queue_conf'', the job is killed with SIGKILL, not with SIGSEGV. Note that ''h_vmem'' specifies the maximal size of **allocated_memory, not used_memory**, in other words it is the VIRT column in ''top'', not the RES column. SGE does not use this parameter in any other way. Notably, job scheduling is not affected by this parameter and therefore there is no guarantee that there will be this amount of memory on the chosen machine. The problem is that some programs (e.g. Java with the default setting) allocate much more (virtual) memory than they actually use in the end. If we want to be ultra conservative, we should set ''h_vmem'' to the same value as ''mem_free''. If we want to be only moderately conservative, we should specify something like h_vmem=1.5*mem_free, because some jobs will not use the whole mem_free requested, but still our job will be killed if it allocated much more than declared. The default effectively means that your job has no limits. |
| * It is recommended to profile your task first, so you can estimate reasonable memory requirements before submitting many jobs with the same task (varying in parameters which do not affect memory consumption). So for the first time, declare mem_free with much more memory than expected and ssh to a given machine and check ''htop'' (sum all processes of your job) or (if the job is done quickly) check the epilog. When running other jobs of this type, set ''mem_free'' (and ''act_mem_free'' and ''h_vmem'') so you are not wasting resources, but still have some reserve. | * It is recommended to **profile your task first**, so you can estimate reasonable memory requirements before submitting many jobs with the same task (varying in parameters which do not affect memory consumption). So for the first time, declare mem_free with much more memory than expected and ssh to a given machine and check ''htop'' (sum all processes of your job) or (if the job is done quickly) check the epilog. When running other jobs of this type, set ''mem_free'' (and ''act_mem_free'' and ''h_vmem'') so you are not wasting resources, but still have some reserve. |
| * **s_vmem** is similar to ''h_vmem'', but instead of SIGSEGV/SIGKILL, the job is sent a SIGXCPU signal which can be caught by the job and exit gracefully before it is killed. So if you need it, set ''s_vmem'' to a lower value than ''h_vmem'' and implement SIGXCPU handling and cleanup. | * **s_vmem** is similar to ''h_vmem'', but instead of SIGSEGV/SIGKILL, the job is sent a SIGXCPU signal which can be caught by the job and exit gracefully before it is killed. So if you need it, set ''s_vmem'' to a lower value than ''h_vmem'' and implement SIGXCPU handling and cleanup. |
| |
| ===== Advanced usage ===== | ===== Advanced usage ===== |
| |
| | * <code>qsub -o LOG.stdout -e LOG.stderr</code> |
| | redirect std{out,err} to separate files with given names |
| | |
| <code> | <code> |
| qsub -o LOG.stdout -e LOG.stderr | |
| # to redirect std{out,err} to separate files with given names | |
| qsub -S /bin/bash | qsub -S /bin/bash |
| # Choose the interpreter of your script. I think ''/bin/bash'' is now (2017/09) the default (but it used to be ''csh''). | # Choose the interpreter of your script. I think ''/bin/bash'' is now (2017/09) the default (but it used to be ''csh''). |
| qsub -v PATH | qsub -v PATH |
| # | # export a given environment variable from the current shell to the job |
| qsub -V | qsub -V |
| # když chcete předat proměnné prostředí | # export all environment variables |
| man qsub qstat qhold queue_conf sge_types complex | man qsub qstat qhold queue_conf sge_types complex |
| # Find out all the details missing here. You'll have to do it one anyway. | # Find out all the gory details which are missing here. You'll have to do it one anyway:-). |
| </code> | </code> |
| |
| * By default, all the resource requirements (specified with ''-l'') and queue requirements (specified with ''-q'') are //hard//, i.e. your job won't be scheduled unless they can be fulfilled. You can use **''-soft''** to mark all following requirements as nice-to-have. And with **''-hard''** you can switch back to hard requirements. | * By default, all the resource requirements (specified with ''-l'') and queue requirements (specified with ''-q'') are //hard//, i.e. your job won't be scheduled unless they can be fulfilled. You can use **''-soft''** to mark all following requirements as nice-to-have. And with **''-hard''** you can switch back to hard requirements. |
| * If you often run (ad-hoc) bash commands via ''qsub'', check two alternative qsub wrappers ''~bojar/tools/shell/qsubmit'' or ''~stepanek/bin/qcmd'', which allow you to enter the command on command line without creating any temp script files. The wrappers have also other features (some qsub options have changed default values). ''qcmd'' is older, but unlike ''qsubmit'' it has POD documentation, correct time computation and you don't need to quote the command. | * If you often run (ad-hoc) bash commands via ''qsub'', check two alternative qsub wrappers ''~bojar/tools/shell/qsubmit'' or ''~stepanek/bin/qcmd'', which allow you to enter the command on command line without creating any temp script files. The wrappers have also other features (some qsub options have changed default values). ''qcmd'' is older, but unlike ''qsubmit'' it has POD documentation, correct time computation and you don't need to quote the command. |
| |
| ===== Monitorování úloh ===== | ===== Monitorování úloh ===== |
