dragnet:cluster_usage

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision		 Previous revision
dragnet:cluster_usage [2015-12-22 17:46] – typos amesfoortdragnet:cluster_usage [2019-01-07 15:06] (current) – [Access and Login] Reinoud Bokhorst
Line 1: Line 1:
 ====== DRAGNET Cluster Usage ====== ====== DRAGNET Cluster Usage ======
  
-Hope this helps... If not let me (Alexander) know (amesfoort@astron.nl).+Some non-obvious and DRAGNET hardware and setup specific info on using DRAGNET wrt logins, (fast) network transfers, cluster-wide commands and compute job submission / scheduling via SLURM. 
 + 
 +Feel free to extend / improve!
  
  
 ===== Access and Login ===== ===== Access and Login =====
-To get an account, ask Jason Hessels (''hessels@astron.nl'').\\ +To get an account, get permission from the Dragnet PI: Jason Hessels (''hessels[AT]astron[DOT]nl'').\\ 
-With permission from Jason, ask Teun Grit (''grit@astron.nl'') to add access to DRAGNET (via NIS). If you don't have access to the LOFAR portal, tell him. Idem for the ASTRON portal, i.e. if you are not working for ASTRON.+Easiest is to ask him to send his permission to the RO Sysadmins (''roadmin[AT]astron[DOT]nl'') for a LOFAR NIS account to access the LOFAR portal, and to Mike Sipior (''sipior[AT]astron[DOT]nl'') to add your account to DRAGNET.\\ 
 +You can also provide RO Admin your (e.g. home) IP(s) to add to a LOFAR portal white list if needed.
  
-Having an account, ssh to hostname ''dragnet.control.lofar'' or easier, just **''dragnet''**, from the LOFAR portal (or tunnel through it): +Having an account, ssh to hostname ''dragnet.control.lofar'' or easier, just **''dragnet''**, from the LOFAR portal (''portal.lofar.eu'') (or tunnel through it): 
-  ssh USERNAME@dragnet+  $ ssh USERNAME@dragnet
  
  
 ==== Password-less Login ==== ==== Password-less Login ====
 Within the cluster (or even to it), don't bother typing your password all the time. Passwords make cluster-wide commands a nightmare. Instead, use an ssh key pair: Within the cluster (or even to it), don't bother typing your password all the time. Passwords make cluster-wide commands a nightmare. Instead, use an ssh key pair:
-  ssh-keygen -t rsa  # or copy an existing public key pair to .ssh/ +  $ ssh-keygen -t rsa  # or copy an existing public key pair to .ssh/ 
-  cat .ssh/id_rsa.pub >> .ssh/authorized_keys +  $ cat .ssh/id_rsa.pub >> .ssh/authorized_keys 
-  chmod 600 .ssh/authorized_keys+  $ chmod 600 .ssh/authorized_keys 
 +(For completeness: Your .ssh/id_rsa contains your private key. Do **not** share it with others. If compromised, asap regenerate the key pair. (This may not be enough if someone else already misused it...)
  
-Now test if this works by logging in and out to ''drg01'' without entering a password (this should succeed with no output): +To make login between nodes more reliable, you can disable the ssh host identification verification within DRAGNET. 
-  ssh drg01 exit+It is overkill within our cluster and if we ever need to reinstall a node, its key fingerprint will then change, causing your (auto-)login to fail until you manually remove the offending entries from ''.ssh/known_hosts''. \\ 
 +To disable, add to (or create) your ''.ssh/config'' file on DRAGNET: 
 +  NoHostAuthenticationForLocalhost yes 
 +   
 +  Host dragnet dragnet.control.lofar dragproc dragproc-10g dragproc.control.lofar dragproc-10g.online.lofar drg?? drg??.control.lofar drg??-10g drg??-10g.online.lofar drg??-ib drg??-ib.dragnet.infiniband.lofar 
 +  StrictHostKeyChecking no
  
-(For completeness: Your .ssh/id_rsa contains your private key. Do **not** share it with others. If compromised, asap change your password and regenerate the key pair.)+Now test if password-less login works by logging in and out to ''drg23'' without entering a password (this should succeed with no output): 
 +  ssh drg23 exit
  
 +===== Finding Applications =====
 +To use most applications conveniently, you need to set or extend environment variables, such as PATH, LD_LIBRARY_PATH, PYTHONPATH, ... Unlike CEP clusters that use the home brew ''use <pkg>'' command, we use the ''module <command> [pkg]'' command. (Some users just export the needed values explicitly.)
  
-===== Hostname Hell and Routing Rampage ===== 
-If you are just running some computations on DRAGNET, skip this section. But if you need fast networking, or are already deep in the slow data transfers and rapid-fire connection errors, here is some info that may save you time wrt the multiple networks and network interfaces. (Or just tell us your needs.) 
  
-=== Hostnames === +==== Practical Summary ==== 
-  * dragnet(.control.lofar) +On DRAGNET add to your .bashrc e.g.: 
-  * dragproc(.control.lofar) +  module add local-user-tools lofar casacore 
-  * drg01(.control.lofar) - drg23(.control.lofar)+or a similar list (''casacore'' contains python-casacore aka pyrap).
  
-=== Networks === +Command to print the list to select from: 
-  Control/Management network: NODENAME.control.lofar (1 Gb) (all nodes) +  $ modules avail 
-  10G network:                NODENAME-10g.online.lofar (10 Gb) (all drgXX nodes and ''dragproc'') +Re-login (or enter the ''module add <pkgs>'' command) to apply in each login session. (If you use the screen(1) program, restart it too!)
-  Infiniband network (IPoIB): NODENAME-ib.dragnet.infiniband.lofar (56 Gb) (all drgXX nodes) +
-(There is also a 1 Gb IPMI network.)+
  
-==== Cross-Cluster ==== +If you want to keep using the same tool version instead of auto-upgrading along when updates are installed, then specify the versioned module name (when available), e.g. ''lofar/2.21.1'' or ''casa/4.7''
-When going cross-cluster, prefer to use the fully-qualified domainnames (FQDN), esp. in scripts or programs (i.e. drg11-10g.online.lofar instead of just drg11). See ''/etc/hosts'' on any node for the list.+
  
-In most cases, you will use the network as deduced from the destination hostname or IP. Indicate a 10G name to use the 10G network. Idem for infiniband (IPoIB). (Exception: CEP 2, see below.) 
  
-//Note//: Copying large data sets at high bandwidth to/from other clusters (in particular CEP 2) may interfere with running observations as long as CEP 2 is still in use. If you are unsure, ask us. It is ok to use potentially oversubscribed links heavily, but please coordinate with Science Support!+==== Using the Environment Modules ==== 
 +The "environment values" is a set of key-value pairs per program, inherited from the program that started it. Each shell has its own copy (so if you change one, others are unaffected). 
 +Your environment is copied and adjusted at login. 
 +You can further adjust it in .bashrc (Note that there is also .bash_profile and .profile. What to change for different login types varies among Linux distros and shells and documentation is not always matching reality...)
  
 +The complete, sorted list (1000s of lines) and (unexported) shell variables can be printed by typing ''set''.
  
-=== CEP 2 === +Type ''module help'' for a list of ''module'' commands.
-Initiate connections for e.g. data transfers from CEP 2 to HOSTNAME-10g.online.lofar and you will go over 10G.+
  
-The reverse, connecting from DRAGNET to CEP 2, by default will connect you via DRAGNET 1G (e.g. for login). To use 10G (e.g. to copy datasets), you need to bind to the local 10G interface name or IP. The program you are using has to support this via e.g. a command-line argument.+List of available modules (July 2017): 
 +  $ module avail 
 +   
 +  --------------------------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------------------------- 
 +  dot         module-git  module-info modules     null        use.own 
 +   
 +  ---------------------------------------------------------------------------- /etc/modulefiles ----------------------------------------------------------------------------- 
 +  aoflagger/2.8.0    casa/4.7           casacore/2.0.3     casarest/current   cuda/current       lofar/2.20.0       lofardal/2.5.0     srm/2.6.28         wsclean/current 
 +  aoflagger/2.9.0    casa/5.0           casacore/2.1.0     cuda/7.0           karma/1.7.25       lofar/2.21.1       lofardal/current   wsclean/1.12 
 +  aoflagger/current  casa/current       casacore/current   cuda/7.5           local-user-tools   lofar/2.21.5       mpi/mpich-x86_64   wsclean/2.2.1 
 +  casa/4.6           casacore/2.0.1     casarest/1.4.1     cuda/8.0           lofar/2.17.5       lofar/current      mpi/openmpi-x86_64 wsclean/2.4 
 + 
 +Add latest lofar module to your env: 
 +  $ module add lofar   # or a specific one e.g. module add lofar/2.17.5 
 + 
 +Remove module from your env (e.g. if it conflicts with another version you want to use): 
 +  $ module rm lofar 
 +  $ module purge  # remove all added modules 
 + 
 +To run the prefactor and factor imaging pipelines, you may want to only use the following command (do not add ''casa''). (And ensure your pipeline.cfg refers to the same paths.) 
 +  $ module add local-user-tools wsclean/2.4 aoflagger/2.9.0 lofar/2.21.1 casarest/1.4.1 casacore/2.1.0 
 +If you login and want to use CASA instead, better run ''/usr/local/casa-release/bin''. You may also remove (i.e. purge) all added modules and add the ''casa'' module, but it only sets PATH, which then may find CASA's own ''bin/python'' and ''bin/ipython'', which interferes easily with other tools. 
 + 
 +See what adding the ''local-user-tools'' module does (Aug 2016): 
 +  $ module show local-user-tools 
 +  ------------------------------------------------------------------- 
 +  /etc/modulefiles/local-user-tools: 
 +   
 +  module-whatis Adds tools, libraries and Python modules under /usr/local to your environment. 
 +    Pulsar tools : dspsr, psrcat, psrdada, pstfits, psrchive, tempo, tempo2, dedisp, sigproc, ffasearch, ephem, see, clig, ... 
 +    Imaging tools: factor, losoto, ds9, Duchamp, sagecal, excon imager, rmsynthesis, pyselfcal, ...  
 +  prepend-path PATH /usr/local/bin  
 +  prepend-path PYTHONPATH /usr/local/lib/python2.7/site-packages:/usr/local/lib64/python2.7/site-packages 
 +  -------------------------------------------------------------------
  
  
Line 65: Line 107:
  
 Example: Example:
-  cexec drg:3-5 "df -h"    # disk usage on the drg04(!), drg05, drg06(!) nodes +  $ cexec drg:3-5 "df -h"    # disk usage on the drg04(!), drg05, drg06(!) nodes 
-  cexec dragnet:23 ls      # run ls on dragproc +  $ cexec dragnet:23 ls      # run ls on dragproc 
-  cexec hostname           # hostnames as seen from each cluster node+  $ cexec hostname           # hostnames as seen from each cluster node
  
 The hostname specifier (2nd optional argument) must contain a ':' and may also be ''drg'', which excludes the ''dragproc'' node. The hostname specifier (2nd optional argument) must contain a ':' and may also be ''drg'', which excludes the ''dragproc'' node.
-The ''dragnet'' hostname specifier contains all nodes (incl head node). The ''drg'' group is without ''dragproc''. (It is not possible to define a C3 group without the head node.)+The ''dragnet'' hostname specifier contains all nodes (incl head node). The ''drg'' group is without ''dragproc''. The head node is never part of the group, though you can explicitly specify it if needed e.g. in scripts.
 Note that the hostname numbers here specify start and end index (starting at 0!). Note that the hostname numbers here specify start and end index (starting at 0!).
  
Line 78: Line 120:
  
 Examples of simple commands: Examples of simple commands:
-  ansible alldragnet -a 'df -h'                                  # disk usage on all nodes +  $ ansible alldragnet -a 'df -h'                                  # disk usage on all nodes 
-  ansible 'proc;workers' -f 25 -a 'df -h /data1 /data2'          # disk usage on dragproc and worker nodes, connect to max 25 nodes at a time +  $ ansible proc:workers -f 25 -a 'df -h /data1 /data2'            # disk usage on dragproc and worker nodes, connect to max 25 nodes at a time 
-  ansible workers -f 25 -a 'ls -al /data1/LOBSID /data2/LOBSID'  # list /data*/LOBSID files on all drg* nodes, connect to max 25 nodes a time +  $ ansible workers -f 25 -a 'ls -al /data1/LOBSID /data2/LOBSID'  # list /data*/LOBSID files on all drg* nodes, connect to max 25 nodes a time 
-  ansible 'drg01;drg17' -a 'ls -l /data1'                        # list /data1 on drg01 and drg17 +  $ ansible drg01:drg17 -a 'ls -l /data1'                          # list /data1 on drg01 and drg17 (not drg01 till drg17) 
-Apart from hostnames, the following hostname groups are recognized on DRAGNET: ''head'', ''proc'', ''workers'', ''alldragnet''. +Apart from hostnames, the following hostname groups are also recognized on DRAGNET: ''head'', ''proc'', ''workers'', ''alldragnet'', ''all'' (last two are the same). 
- +The command must be a simple command. It can be the name of an executable shell script if accessible to all hosts, but not a compound shell command with &, &&, pipes or other descriptor redirection (you can of course run the shell with some argument, but then, what's the point of using ansible like that?).
-The command must be a simple command. It can be the name of an executable shell script if accessible to all hosts, but not a compound shell command with &, &&, pipes or other descriptor redirection (you can of course run the shell with some argument, but then, what's the point of using ansible?).+
  
 Background: Ansible heavily relies on the idea to specify what you want in terms of the desired situation rather than what to do to get there. Such //idempotent// commands work correctly regardless whether some nodes are already ok or different. To this end ansible has numerous modules to manipulate system settings in an easy way, but you can also write your own modules (e.g. to reinstall (parts of) a type of node), or so-called //playbooks// to manage configuration and deployment. Background: Ansible heavily relies on the idea to specify what you want in terms of the desired situation rather than what to do to get there. Such //idempotent// commands work correctly regardless whether some nodes are already ok or different. To this end ansible has numerous modules to manipulate system settings in an easy way, but you can also write your own modules (e.g. to reinstall (parts of) a type of node), or so-called //playbooks// to manage configuration and deployment.
Line 92: Line 133:
 ==== Shell Loop and SSH ==== ==== Shell Loop and SSH ====
 Examples: Examples:
-  for ((i = 1; i <= 10; i++)); do host=$(printf drg%02u $i); ssh $host "df -h"; done  # disk usage on the drg01-drg10 nodes +  $ for host in $(seq -f drg%02g 1 10); do ssh $host "hostname && df -h /data1 /data2"; done  # disk usage on the drg01-drg10 nodes 
-  for host in drg01 drg17; do ssh $host "df -h"; done                                 # disk usage on drg01 and drg17+  $ for host in drg01 drg17; do ssh $host "df -h"; done                                       # disk usage on drg01 and drg17
  
 Be careful with complex commands! Be careful with complex commands!
  
 +
 +===== Data Copying =====
 +Generic data copying info plus cluster specific subsections.
 +
 +To copy large data sets between nodes or into / out of DRAGNET, you can use ''scp'' or ''sftp'' or ''rsync''. However, these tools are unable to fill links well in excess of 1 Gb/s. For multiple large files, you can start several transfers, but this may not be enough and is tedious. Single core CPU power may also be a problem. To alleviate CPU load, select the simple ''arcfour'' cipher (it's not possible to select no ''scp'' cipher).
 +  $ scp -B -c arcfour <src_node:path> <dst_node:path>
 +
 +The ''bbcp'' tool is able to utilize more bandwidth. It first uses ''ssh'' to login and then starts ''bbcp'' on both sides. Example command we use to copy all files in a directory to CEP3 node lof003:
 +  $ bbcp -A -e -s 4 -B 4M -r -g -@ follow -v -y dd -- drg23-10g.online.lofar:/data1/xxx/cs/ lof003.offline.lofar:/data/projects/xxx/Lyyyyyy/cs/
 +
 +Notes:
 +  * OpenSSH-6.7 no longer allows the ''arcfour'' cipher, but DRAGNET uses 6.6. (Both sides of the transfer must allow it.)
 +  * The ''rsync'' tool remains great to retransfer (or check if) data changed in minor ways, as ''rsync'' only syncs (chunks around) the changes. ''rsync'' is also great to transfer many small files.
 +  * For ''bbcp'', if you want to see network speed, drop the "-y dd" option to flush.
 +
 +
 +==== Hostname Hell and Routing Rampage ====
 +If you are just running some computations on DRAGNET, skip this section. But if you need fast networking, or are already deep in the slow data transfers and rapid-fire connection errors, here is some info that may save you time wrt the multiple networks and network interfaces. (Or just tell us your needs.)
 +
 +==== Hostnames ===
 +Control network:
 +  * dragnet(.control.lofar)
 +  * dragproc(.control.lofar)
 +  * drg01(.control.lofar) - drg23(.control.lofar)
 +
 +10G network:
 +  * dragproc-10g(.online.lofar)
 +  * drg01-10g(.online.lofar) - drg23-10g(.online.lofar)
 +
 +Infiniband network (~54G):
 +  * drg01-ib(.dragnet.infiniband.lofar)
 +
 +(There is also a 1 Gb IPMI network.)
 +
 +Note that for copying files between hard disks, there is some benefit to use the 10G network. If you have data to copy on ''/data1'' and ''/data2'', transfer from/to both areas in parallel. This will not reach 10 Gb/s, so using infiniband for such transfers does not help.
 +
 +
 +==== Cross-Cluster ====
 +When writing scripts that (also) have to work cross-cluster, prefer to use the fully-qualified domain names (FQDN) (e.g. ''drg23-10g.online.lofar'' instead of just ''drg23''). See ''/etc/hosts'' on any node for the list.
 +
 +In most cases, you will use the network as deduced from the destination hostname or IP. Indicate a 10G name to use the 10G network. Idem for infiniband. (Exception: CEP 2, see below.)
 +
 +//Note//: Copying large data sets at high bandwidth to/from other clusters (in particular CEP 2) may interfere with running observations as long as CEP 2 is still in use. If you are unsure, ask us. It is ok to use potentially oversubscribed links heavily, but please coordinate with Science Operations and Support!
 +
 +
 +=== CEP 2 ===
 +Initiate connections for e.g. data transfers from CEP 2 to HOSTNAME-10g.online.lofar to transfer via 10G.
 +
 +The reverse, connecting from DRAGNET to CEP 2, by default will connect you via DRAGNET 1G (e.g. for login). To use 10G (e.g. to copy datasets), you need to bind to the local 10G interface name or IP. The program you are using has to support this via e.g. a command-line argument.
 +
 +
 +=== CEP 3 ===
 +Use the ''lofXXX.offline.lofar'' hostnames to transfer via 10G.
 +
 +
 +=== CEP 4 ===
 +CEP 4 has a Lustre global file system. Copying data to DRAGNET is supposed to happen via ''lexar003.offline.lofar'' and ''lexar004.offline.lofar''.
 +
 +A Lustre mount has also been set up on DRAGNET, but the storage name is not mounted by default.
 +
 +
 +=== External Hosts (also LTA Staged Data) ===
 +
 +To copy data sets from outside the LOFAR network (e.g. staged long-term archive data) into DRAGNET, there is unfortunately only 1 Gbit/s available that is shared with other LOFAR users. A 10G link may become available in the future.
 +
 +There are 3 cases to distinguish:
 +
 +== 1. Access external hosts (but not lofar-webdav.grid.sara.nl) from the LOFAR network ==
 +This all uses the LOFAR portal / public internet link (1 Gbit/s). Since the LOFAR portal is used by all users to login, it is important not to overload it. Load is monitored and too hungry copying processes may be killed if they harm other users.
 +
 +So please rate-limit your download from outside into DRAGNET and CEPx! A reasonable chunk of 1 Gbit/s is 400 Mbit/s (= 50 MByte/s), such that if somebody else does this too, there is still a bit of bandwidth for dozens of login sessions from other users. (Yes, this is hardly a foolproof strategy.) Please use:
 +  $ scp -l 400000 ...         # value in kbit/s
 +  or
 +  $ wget --limit-rate=50m ... # value in MByte/s
 +  or
 +  $ curl --limit-rate=50m ... # value in MByte/s
 +  or
 +  $ rsync --bwlimit=51200 ... # value in kByte/s  
 +
 +For those interested, you can use ''atop 2'' on the LOFAR portal as a regular user to see the currently routed traffic rate across the network interfaces. More details on a single DRAGNET node can be monitored by administrating users using the ''nethogs'' program. Everyone can see a lot of cluster performance metrics on http://ganglia.astron.nl/ (select ''dragnet'').
 +
 +== 2. Download via http(s) from lofar-webdav.grid.sara.nl to the LOFAR network ==
 +
 +A http(s) ''squid'' proxy server has been set up to forward the traffic over a special line to SurfSara. This activates when you set the ''http_proxy'' **and** ''https_proxy'' environment variables correctly before starting the download. (Both are needed as the **https** results in a redirect to a plain **http** URL.) Like so:
 +
 +  http_proxy=lexar004.control.lofar:3128 https_proxy=lexar004.control.lofar:3128 wget --no-check-certificate https://lofar-webdav.grid.sara.nl/...
 +
 +//However//, atm you need to authenticate to this proxy. Get an account via the ASTRON "Science Operations & Support" group <sos[AT]astron[DOT]nl> (sigh...)\\
 +Put that username and password in a ''.wgetrc'' file in your home directory:
 +  proxy-user=yourusername
 +  proxy-password=yourpassword
 +then keep it reasonably private by making that file only accessible to you:
 +  chmod 600 ~/.wgetrc
 +
 +If you use this only for lofar-webdav.grid.sara.nl, you do not need to rate-limit your downloads as specified above. (Hence, better set it on the command-line as shown above instead of exporting it to your environment where it always applies.)\\
 +
 +//Note:// This also works for other http(s) destinations than SurfSara servers, however, then you need to rate-limit your http(s) traffic as described above under **1.**. Do **not** use this for other LTA sites than SurfSara, as atm this interferes with data streams from some int'l station!
 +
 +== 3. Between ASTRON internal 10.xx.xx.xx nodes and the LOFAR network ==
 +Specifically for ASTRON hosts with an internal ''10.xx.xx.xx'' IP, you can access nodes in the LOFAR control network directly by IP to copy data at 1 Gbit/s without going through the portal.lofar.eu node. There is no need to rate-limit this, the network will divide bandwidth among transfers when needed.
 ===== SLURM Job Submission ===== ===== SLURM Job Submission =====
  
Line 104: Line 245:
   * SLURM does not enforce accessing nodes through it; one can access any node via ssh. Depending on the intention and the current workload, that may be fine or less desirable.   * SLURM does not enforce accessing nodes through it; one can access any node via ssh. Depending on the intention and the current workload, that may be fine or less desirable.
   * SLURM has a ton of options that we haven't all set up. In particular, atm it does not enforce exclusive access to GPUs via cgroups (although it does set ''CUDA_VISIBLE_DEVICES'' if you explicitly request GPUs). Once a node is (partially) assigned to your program, your program can in principle use any resource on that node.   * SLURM has a ton of options that we haven't all set up. In particular, atm it does not enforce exclusive access to GPUs via cgroups (although it does set ''CUDA_VISIBLE_DEVICES'' if you explicitly request GPUs). Once a node is (partially) assigned to your program, your program can in principle use any resource on that node.
- 
-If you are having trouble using SLURM, please contact Alexander (amesfoort@astron.nl). 
  
 ==== Introduction: the trivial stuff ==== ==== Introduction: the trivial stuff ====
 From any DRAGNET node (typically the ''dragnet'' head node), you can submit compute (or perhaps also separate data transfer) jobs. From any DRAGNET node (typically the ''dragnet'' head node), you can submit compute (or perhaps also separate data transfer) jobs.
  
-Run a single task, see output as it is produced, and wait for completion. Note that in this case the ''ls'' program must be available on any node that may be used. +Use ''srun'' to start a task, see output as it is produced, and wait for completion. Use resource options such as %%--%%nodes=10 or %%--%%tasks=10, and/or %%--%%nodelist=drg01 to reserve nodes or CPUs (see below or ''man srun'' for more info). 
-  $ srun -n 1 ls dir1 dir2 +  $ srun --nodes=5 --nodelist=drg01,drg02 ls -l /data1 /data2 
-  file1 +  dir1 dir2 file1 file2 [...] 
-  file2 + 
-  [...]+Use ''sbatch'' to queue a job to run a supplied batch script with various commands, advanced options, and resource specifications in shell comments (see below). (No need to also use the ''screen'' command.) Slurm immediately prints the JobId and returns. It redirects stdout and stderr to a slurm-<JobId>.log file. For simple cases, auto-generate the script using %%--%%wrap.  
 +  $ sbatch --mail-type=END,FAIL --mail-user=your-email-addr@example.com --wrap="ls -l /data1 /data2" 
 +  Submitted batch job <JobId> 
 +The ''srun'' and ''sbatch'' mostly take the same args, so likely, you want to combine the 2 examples above using ''sbatch'' and the resource options, or better, supply a simple shell script. 
 +\\ 
 +Tip: use absolute path names and $HOME.
  
 \\ \\
Line 127: Line 271:
              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
                  9   workers       ls amesfoor CD       0:01      1 drg                  9   workers       ls amesfoor CD       0:01      1 drg
 +
 +\\
 +Show details of a specific job:
 +  $ scontrol show job <JobId>
 +  JobId=223058 JobName=wrap
 +     [<~20 lines of info on status, resources, times, directories, ...>]
  
 \\ \\
 Show list and state of nodes. When submitting a job, you can indicate one of the partitions listed or a (not necessarily large enough) set of nodes that must be used. Please hesitate indefinitely when trying to submit insane loads to the ''head'' partition. :) Show list and state of nodes. When submitting a job, you can indicate one of the partitions listed or a (not necessarily large enough) set of nodes that must be used. Please hesitate indefinitely when trying to submit insane loads to the ''head'' partition. :)
-  $ sinfo+  $ sinfo --all
   PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST   PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
-  workers*     up   infinite     23   idle drg[01-23] +  workers*     up   infinite     24   idle dragproc,drg[01-23]
-  proc         up   infinite      1   idle dragproc+
   head         up   infinite      1   idle dragnet   head         up   infinite      1   idle dragnet
 +  lofarobs     up   infinite     24   idle dragproc,drg[01-23]    # Note: for observations; use 'sinfo --all', else only usable & visible for users in lofarsys group (+ slurm,root)
 If you get an error on job submission that there are no resources in the cluster to ever satisfy your job, and you know this is wrong (no typo), you can see with the ''sinfo'' if there are nodes out of service. (SLURM may remove a node from a partition on misconfiguration or hardware malfunctioning.) If you get an error on job submission that there are no resources in the cluster to ever satisfy your job, and you know this is wrong (no typo), you can see with the ''sinfo'' if there are nodes out of service. (SLURM may remove a node from a partition on misconfiguration or hardware malfunctioning.)
  
 +\\
 +More detail:
 +  $ sinfo -o "%10N %8z %8m %40f %10G %C"
 +  NODELIST   S:C:T    MEMORY   AVAIL_FEATURES                           GRES       CPUS(A/I/O/T)
 +  dragnet,dr 1+:4+:1  31800+   (null)                                   (null)     0/20/0/20
 +  drg[01-23] 2:8:1    128500   (null)                                   gpu:4      0/368/0/368
 +where in the last column A = Allocated, I = Idle, O = Other, T = Total
 ==== Hints on using more SLURM capabilities ==== ==== Hints on using more SLURM capabilities ====
 The sbatch(1) command offers to: The sbatch(1) command offers to:
Line 149: Line 306:
   * either number of nodes or CPUs   * either number of nodes or CPUs
   * number of GPUs, if any needed. If no GPUs are requested, any GPU program will fail. (Btw, this policy is not fully as intended, so if technically it can be improved, we can look into it.)   * number of GPUs, if any needed. If no GPUs are requested, any GPU program will fail. (Btw, this policy is not fully as intended, so if technically it can be improved, we can look into it.)
-You do not have to indicate memory size, but if you don't, SLURM will grant you all the memory of a node, preventing other jobs from running on the same node(s). This may or may not be the intention. (If the intention, better use %%--%%exclusive.)+  * In general, but no longer on DRAGNET or CEP4: if you want to run >1 job on a node at the same time, memory. Just reserve per job: 128500 / NJOBS_PER_NODE. By default, SLURM reserves all the memory of a node, preventing other jobs from running on the same node(s). This may or may not be the intention. (If the intention, better use %%--%%exclusive.)
  
-Note that a ''CPU'' is to SLURM a hardware resource that the OS can schedule a task on. This is typically a hardware thread, or if no hyperthreading, a CPU core.+Note that a ''CPU'' is to SLURM a hardware resource that the OS can schedule a task on. On DRAGNET it is a CPU core (16 on all nodes, but 4 on the head node). (On typical SLURM installs, it's a hardware thread, but we don't expect to get something out of HyperThreading.)
  
-To indicate a scheduling resource constraint on 2 GPUs, use the --gres option (//gres// stands for //generic resource//):+To indicate a scheduling resource constraint on 2 GPUs, use the %%--%%gres option (//gres// stands for //generic resource//):
   $ srun --gres=gpu:2 -n 1 your_gpu_prog   $ srun --gres=gpu:2 -n 1 your_gpu_prog
  
 To indicate a list of nodes that must be used (list may be smaller than number of nodes requested). Some examples: To indicate a list of nodes that must be used (list may be smaller than number of nodes requested). Some examples:
-  $ srun --nodelist=drg02 ls +  $ srun --nodelist=drg23 ls 
-  $ srun --nodelist=drg05-drg07,drg22 -n 8 ls+  $ srun --nodelist=drg05-drg07,drg23 -n 8 ls
   $ srun --nodelist=./nodelist.txt ls   # with a '/' in the arg value   $ srun --nodelist=./nodelist.txt ls   # with a '/' in the arg value
  
-For the moment, see more explanation and examples at http://www.umbc.edu/hpcf/resources-tara-2013/how-to-run.php+For the moment, see more explanation and examples at http://hpcf.umbc.edu/how-to-run-programs-on-maya/
  
 Please see the manual pages on srun(1), sbatch(1), salloc(1) and the [[http://slurm.schedmd.com/|SLURM website]] for more info. Please see the manual pages on srun(1), sbatch(1), salloc(1) and the [[http://slurm.schedmd.com/|SLURM website]] for more info.
 +
 +==== SLURM Cluster Management ====
 +Some commands I looked up and probably need again another time.
 +
 +Bring fixed node back to partition from state DOWN to state IDLE (logged in as slurm):
 +  $ scontrol update NodeName=drg23 state=idle
 +
 +Users can resume their (list of) job(s) after SLURM found it/they cannot be run (network errors or so) and sets the status to something like 'launch failed, requeued held'. If the range is sparse, slurm prints some errors, but does resume all existing jobs.\\
 +This can also be executed by users for their own jobs.
 +  $ scontrol resume 100
 +  $ scontrol resume [1000,2000]
 +  
 +==== SLURM Troubleshooting ====
 +== "Undraining" nodes ==
 +
 +If you expect that there should be enough resources, but slurm submission fails because some nodes could be in "drain" state, you can check that by running "sinfo". You could see 
 +something like this, where nodes drg06 and drg08 are in drain state:
 +
 +  $ sinfo
 +  PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
 +  workers*     up   infinite      2  drain drg[06,08]
 +  workers*     up   infinite      1    mix drg01
 +  workers*     up   infinite     21   idle dragproc,drg[02-05,07,09-23]
 +  head         up   infinite      1   idle dragnet
 +
 +To "undrain" e.g. drg08, you can do:
 +  $ scontrol update NodeName=drg08 State=DOWN Reason="undraining"
 +  $ scontrol update NodeName=drg08 State=RESUME
 +
  • Last modified: 2015-12-22 17:46
  • by amesfoort