| Both sides previous revision
Previous revision
Next revision
|
Previous revision
Next revision
Both sides next revision
|
grid [2018/03/01 22:04]
kruza [Advanced usage] |
grid [2018/04/25 21:28]
popel all flags in a comment |
| ==== MS = Malá Strana (ms-all.q) ==== | ==== MS = Malá Strana (ms-all.q) ==== |
| |
| ^ Name ^ CPU type ^ GHz ^cores ^RAM(GB)^ note ^ | ^ Name ^ CPU type and flags ^ GHz ^cores ^RAM(GB)^ note ^ |
| | andromeda[1-13] | AMD 2xCore4 Opteron | 2.8 | 8 | 32 | | | | andromeda[1-13] | AMD Opteron | 2.8 | 8 | 32 | | |
| | hydra[1-4] | AMD | 2.6 | 16 | 128 | | | | hydra[1-4] | AMD Opteron SSE4 AVX | 2.6 | 16 | 128 | | |
| | fireball[1-10] |Intel ??2xCore4 Xeon | 3.0 | 4 | 32 | | | | fireball[1-10] | Intel Xeon | 3.0 | 4 | 32 | | |
| | hyperion[1-9] | Intel 2xCore2 Xeon | 3.0 | 4 | 32 | | | | hyperion[1-9] | Intel Xeon | 3.0 | 4 | 32 | | |
| | lucifer[1-10] |Intel ??2xCore4 Xeon | 2.4 | 16 | 128 | | | | lucifer[1-10] | Intel Xeon SSE4 | 2.4 | 16 | 128 | | |
| | orion[1-6] | Intel 2xCore4 Xeon | 2.3 | 8 | 32 | | | | orion[1-6] | Intel Xeon | 2.3 | 8 | 32 | | |
| | orion[7-10] | Intel | 2.0 | 4 | 32 | | | | orion[7-10] | Intel Xeon | 2.0 | 4 | 32 | | |
| | tauri[1-10] |Intel ??2xCore4 Xeon | 3.0 | 4 | 32 | | | | tauri[1-10] | Intel Xeon | 3.0 | 4 | 32 | | |
| | cosmos | Intel 4xCore2 Xeon | 2.9 | 8 | 256 | | | | cosmos | Intel Xeon | 2.9 | 8 | 256 | | |
| | belzebub | Intel 8xCore4 Xeon | 2.9 | 32 | 256 | | | | belzebub | Intel Xeon SSE4 AVX | 2.9 | 32 | 256 | | |
| | iridium |Intel ??2xCore4 Xeon | 1.9 | 16 | 512 | also in ''gpu.q'' | | | iridium | Intel Xeon SSE4 | 1.9 | 16 | 512 | also in ''gpu.q'' | |
| | twister[1,2] | Intel 2xCore4 Xeon | 2.4 | 8 | 48 | also in ''gpu.q'' | | | twister[1,2] | Intel Xeon SSE4 | 2.4 | 8 | 48 | also in ''gpu.q'' | |
| |
| | <html><!-- |
| | sol5 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca lahf_lm dtherm tpr_shadow |
| | sol7 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx tm2 ssse3 cx16 xtpr pdcm dca lahf_lm dtherm tpr_shadow |
| | andromeda4 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc rep_good nopl nonstop_tsc extd_apicid pni monitor cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt hw_pstate npt lbrv svm_lock nrip_save vmmcall |
| | hydra1 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc extd_apicid amd_dcm aperfmperf pni pclmulqdq monitor ssse3 cx16 sse4_1 sse4_2 popcnt aes xsave avx lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 nodeid_msr topoext perfctr_core perfctr_nb arat cpb hw_pstate npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold vmmcall |
| | fireball1 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca lahf_lm dtherm tpr_shadow |
| | hyperion1 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca lahf_lm dtherm tpr_shadow |
| | lucifer1 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat |
| | orion1 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca lahf_lm dtherm tpr_shadow vnmi flexpriority |
| | orion7 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx tm2 ssse3 cx16 xtpr pdcm dca lahf_lm dtherm tpr_shadow |
| | tauri1 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca lahf_lm dtherm tpr_shadow |
| | cosmos fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca lahf_lm dtherm tpr_shadow vnmi flexpriority |
| | belzebub fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm epb kaiser tpr_shadow vnmi flexpriority ept vpid xsaveopt dtherm ida arat pln pts |
| | iridium fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 x2apic popcnt lahf_lm dtherm tpr_shadow vnmi flexpriority ept vpid |
| | twister1 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt lahf_lm ida arat epb dtherm tpr_shadow vnmi flexpriority ept vpid |
| | --> |
| | </html> |
| === Outside LRC cluster (but located as MS) === | === Outside LRC cluster (but located as MS) === |
| ^ Name ^ CPU type ^ GHz ^cores ^ RAM(GB)^ note ^ | ^ Name ^ CPU type ^ GHz ^cores ^ RAM(GB)^ note ^ |
| * 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 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. If you are submitting **more than 100 jobs**, consider using setting them a low priority (e.g. ''-p -1024'', see below) or use [[#qunhold]]. | * 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. If you are submitting **more than 100 jobs**, consider using setting them a low priority (e.g. ''-p -1024'', see below) or use [[#qunhold]] or (even better) [[#array jobs]]. |
| * **Don't submit more than ca 5000 jobs at once**, even if you make sure that at most 100 are running/waiting and the rest is in the //hold// state (e.g. using ''qunhold''). More than 5000 jobs in the queue can overload the SGE, so then no one can execute ''qstat'' (or it takes too long). | * **Don't submit more than ca 5000 jobs at once**, even if you make sure that at most 100 are running/waiting and the rest is in the //hold// state (e.g. using ''qunhold''). More than 5000 jobs in the queue can overload the SGE, so then no one can execute ''qstat'' (or it takes too long). |
| |
| * **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** (see [[#profiling]] below), 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. |
| |
| === qunhold === | === qunhold === |
| ''~stepanek/bin/qunhold'' tries to keep the number of running SGE jobs under a given threshold: all jobs over the threshold are held. If the number of running jobs goes below the threshold (default: 100), 10 jobs (by default) are unheld. Beware: if your jobs submit new jobs, you can get far over the threshold! | ''~stepanek/bin/qunhold'' tries to keep the number of running SGE jobs under a given threshold: all jobs over the threshold are held. If the number of running jobs goes below the threshold (default: 100), 10 jobs (by default) are unheld. Beware: if your jobs submit new jobs, you can get far over the threshold! |
| | |
| | Don't submit more than ca 5000 jobs with qunhold - it overloads the SGE queue and slows done e.g. ''qstat'' (and qunhold uses ''qstat'' internally). |
| |
| === sshcwd === | === sshcwd === |
| |
| If you have a set of tasks (of the same type) and want to run them on multiple machines, use ''qsub -t''. | If you have a set of tasks (of the same type) and want to run them on multiple machines, use ''qsub -t''. |
| * ''-t 1-n'' start array job with n jobs numbered 1 ... n | * ''-t 1-n'' start array job with //n// tasks numbered //1 ... n// |
| * environmental variable ''SGE_TASK_ID'' | * environmental variable ''SGE_TASK_ID'' |
| * output and error files ''$JOB_NAME.[eo]$JOB_ID.$TASK_ID'' | * output and error files ''$JOB_NAME.[eo]$JOB_ID.$TASK_ID'' |
| * ''-t m-n[:s]'' start array job with jobs m, m + s, ..., n | * ''-t m-n[:s]'' start array job with tasks //m, m + s, ..., n// |
| * environmental variables ''SGE_TASK_FIRST, SGE_TASK_LAST, SGE_TASK_STEPSIZE'' | * environmental variables ''SGE_TASK_FIRST, SGE_TASK_LAST, SGE_TASK_STEPSIZE'' |
| * ''-tc j'' run at most j jobs simultaneously | * ''-tc j'' run at most //j// tasks simultaneously |
| * ''-hold_jid_ad comma_separated_job_list'' array jobs that must finish before this job starts; task //i// of the current job depends only on task //i// of the specified jobs | * ''-hold_jid_ad comma_separated_job_list'' array jobs that must finish before this job starts; task //i// of the current job depends only on task //i// of the specified jobs |
| | |
| | If you use ''-tc'', then SGE can handle array jobs of virtually any size. It only starts as many tasks as specified in ''-tc'' at any time, and each scheduling interval (15 seconds in our current configuration) it starts new tasks if less than the specified ''-tc'' limit are running. However, note that it means the maximum throughput is //4 * tc// tasks per minute, so the individual array job tasks need to run for at least tens of seconds for this to be effective. |
| | |
| | The advantage of array jobs over [[#qunhold]] is that it does not overload the SGE job queue. Also if you start an array job, the others can see that it is an array job, how many individual tasks there are and how many of them have already finished. |
| |
| === Delete many jobs at once === | === Delete many jobs at once === |
| * ''cat /SGE/REPORTER/LRC-UFAL/stats/userlist.weight'' -- all users sorted according to their activity (number of submitted jobs × their average duration), updated each night | * ''cat /SGE/REPORTER/LRC-UFAL/stats/userlist.weight'' -- all users sorted according to their activity (number of submitted jobs × their average duration), updated each night |
| * [[http://ufaladm2/munin/ufal.hide.ms.mff.cuni.cz/lrc-headnode.ufal.hide.ms.mff.cuni.cz/index.html|Munin: graph of cluster usage by day and user]] and [[http://ufaladm2/munin/ufal.hide.ms.mff.cuni.cz/apophis.ufal.hide.ms.mff.cuni.cz/index.html|Munin monitoring of Apophis disk server]] (both accessible only from ÚFAL network) | * [[http://ufaladm2/munin/ufal.hide.ms.mff.cuni.cz/lrc-headnode.ufal.hide.ms.mff.cuni.cz/index.html|Munin: graph of cluster usage by day and user]] and [[http://ufaladm2/munin/ufal.hide.ms.mff.cuni.cz/apophis.ufal.hide.ms.mff.cuni.cz/index.html|Munin monitoring of Apophis disk server]] (both accessible only from ÚFAL network) |
| | |
| | ===== Profiling ===== |
| | As stated above, you should always specify the exact memory limits when running your tasks, so that you neither waste RAM nor starve others of memory by using more than you requested. However, memory requirements can be difficult to estimate in advance. That's why you should profile your tasks first. |
| | |
| | A simple method is to run the task and observe the memory usage reported in the epilog, but SGE may not record transient allocations. As documented in ''man 5 accounting'' and observed in ''qconf -sconf'', SGE only collects stats every ''accounting_flush_time''. If this is not set, it defaults to ''flush_time'', which is preset to 15 seconds. But the kernel records all info immediately without polling, and you can view these exact stats by looking into /proc/$PID/status while the task is running. |
| | |
| | You can still miss allocations made shortly before the program exits – which often happens when trying to debug why your program gets killed by SGE after exhausting the reserved space. To record these, use ''/usr/bin/time -v'' (the actual binary, not the shell-builtin command ''time''). Be aware that unlike the builtin, it cannot measure shell functions and behaves differently on pipelines. |
| | |
| | Obtaining peak usage of multiprocess applications is trickier. Detached and backgrounded processes are ignored completely by ''time -v'' and you get the maximum footprint of any children, not the sum of all maximal footprints nor the largest footprint in any instant. |
| | |
| | If you program in C and need to know the peak memory usage of your children, you can also use the ''wait4()'' syscall and calculate the stats yourself. |
| | |
| | If your job is the only one on a given machine, you can also look how much free memory is left when running the job (e.g. with ''htop'' if you know when is the peak moment). |
| | |
| |
| ===== Other ===== | ===== Other ===== |
