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...@@ -32,8 +32,8 @@ General email: ITenDI_Infra-Linux@lumc.nl ...@@ -32,8 +32,8 @@ General email: ITenDI_Infra-Linux@lumc.nl
| Hostname | IP address | CPU | Cores | Memory | GPUs | Purpose | Type machine | | Hostname | IP address | CPU | Cores | Memory | GPUs | Purpose | Type machine |
| --- | --- | --- | --- | --- | --- | --- | --- | | --- | --- | --- | --- | --- | --- | --- | --- |
| res-hpc-lo01 | 145.88.76.243 | Intel E5-2660 | 32 | 128Gb | 0 | Login node | Dell PowerEdge M620 |
| res-hpc-lo02 | 145.88.76.217 | Intel Xe 6248 | 80 | 128Gb | 1 | Login node + Rem Vis* | Dell PowerEdge R740 | | res-hpc-lo02 | 145.88.76.217 | Intel Xe 6248 | 80 | 128Gb | 1 | Login node + Rem Vis* | Dell PowerEdge R740 |
| res-hpc-lo04 | 145.88.76.219 | Intel 8280 | 8 | 32Gb | 0 | Login node | VM |
| res-hpc-exe007 | 145.88.76.220 | Intel E5-2697 | 24 | 384Gb | 0 | Execution node | Dell PowerEdge M620 | | res-hpc-exe007 | 145.88.76.220 | Intel E5-2697 | 24 | 384Gb | 0 | Execution node | Dell PowerEdge M620 |
| res-hpc-exe008 | 145.88.76.224 | Intel E5-2697 | 24 | 384Gb | 0 | Execution node | Dell PowerEdge M620 | | res-hpc-exe008 | 145.88.76.224 | Intel E5-2697 | 24 | 384Gb | 0 | Execution node | Dell PowerEdge M620 |
| res-hpc-exe009 | 145.88.76.222 | Intel E5-2697 | 24 | 384Gb | 0 | Execution node | Dell PowerEdge M620 | | res-hpc-exe009 | 145.88.76.222 | Intel E5-2697 | 24 | 384Gb | 0 | Execution node | Dell PowerEdge M620 |
...@@ -92,7 +92,7 @@ General email: ITenDI_Infra-Linux@lumc.nl ...@@ -92,7 +92,7 @@ General email: ITenDI_Infra-Linux@lumc.nl
## Rules ## Rules
- Always login/connect to the login node **res-hpc-lo01.researchlumc.nl** or **res-hpc-lo02.researchlumc.nl** - Always login/connect to the login node **res-hpc-lo02.researchlumc.nl** or **res-hpc-lo04.researchlumc.nl**
- Always use the workload manager (Slurm) to run/submit jobs or use it interactive - Always use the workload manager (Slurm) to run/submit jobs or use it interactive
- **Never** run a job outside the workload manager (Slurm), not on the login node nor on the execution nodes - **Never** run a job outside the workload manager (Slurm), not on the login node nor on the execution nodes
- **Never** run (heavy) calculations on the login node, but do this on a compute node - **Never** run (heavy) calculations on the login node, but do this on a compute node
...@@ -135,47 +135,48 @@ Other distributions: ...@@ -135,47 +135,48 @@ Other distributions:
#### From the command line (ssh) #### From the command line (ssh)
If your login user name from your Linux workstation is the same as the username on the HPC cluster, you can use: If your login user name from your Linux workstation is the same as the username on the HPC cluster, you can use:
- ssh res-hpc-lo01.researchlumc.nl - ssh res-hpc-lo02.researchlumc.nl
or or
- ssh res-hpc-lo02.researchlumc.nl - ssh res-hpc-lo04.researchlumc.nl
Otherwise: Otherwise:
- ssh username@res-hpc-lo01.researchlumc.nl - ssh username@res-hpc-lo02.researchlumc.nl
or or
- ssh username@res-hpc-lo02.researchlumc.nl - ssh username@res-hpc-lo04.researchlumc.nl
You can make your life easier by editing the file: You can make your life easier by editing the file:
``` ```
vi ~/.ssh/config vi ~/.ssh/config
Host res-hpc-lo01
Hostname 145.88.76.243
User user-name
ServerAliveInterval 60
Host res-hpc-lo02 Host res-hpc-lo02
Hostname 145.88.76.217 Hostname 145.88.76.217
User user-name User user-name
ServerAliveInterval 60 ServerAliveInterval 60
Host res-hpc-lo04
Hostname 145.88.76.219
User user-name
ServerAliveInterval 60
``` ```
Where you adapt the *user-name*. Where you adapt the *user-name*.
#### X11 forwarding #### X11 forwarding
You can show graphical output when you enable X11 forwarding You can show graphical output when you enable X11 forwarding
- ssh -X res-hpc-lo01.researchlumc.nl - ssh -X res-hpc-lo02.researchlumc.nl
or or
- ssh -X res-hpc-lo02.researchlumc.nl - ssh -X res-hpc-lo04.researchlumc.nl
or or
- ssh -Y res-hpc-lo01.researchlumc.nl - ssh -Y res-hpc-lo02.researchlumc.nl
or or
- ssh -Y res-hpc-lo02.researchlumc.nl - ssh -Y res-hpc-lo04.researchlumc.nl
Once you are logged in, you should be able to run a graphical program, for example: Once you are logged in, you should be able to run a graphical program, for example:
- xterm - xterm
...@@ -203,11 +204,11 @@ Go to Session and create a new session: ...@@ -203,11 +204,11 @@ Go to Session and create a new session:
![alt text](images/x2goclient-02.gif "x2goclient-02") ![alt text](images/x2goclient-02.gif "x2goclient-02")
For the **Host**: For the **Host**:
- res-hpc-lo01.researchlumc.nl - res-hpc-lo02.researchlumc.nl
or or
- res-hpc-lo02.researchlumc.nl - res-hpc-lo04.researchlumc.nl
For the **Session type**: For the **Session type**:
- XFCE - XFCE
...@@ -277,7 +278,7 @@ Once you have started the putty program, you will see: ...@@ -277,7 +278,7 @@ Once you have started the putty program, you will see:
![alt text](images/putty-01.gif "putty-01") ![alt text](images/putty-01.gif "putty-01")
Fill in at the Host Name (or IP address): **res-hpc-lo01.researchlumc.nl** or **res-hpc-lo02.researchlumc.nl** Fill in at the Host Name (or IP address): **res-hpc-lo02.researchlumc.nl** or **res-hpc-lo04.researchlumc.nl**
![alt text](images/putty-02.gif "putty-02") ![alt text](images/putty-02.gif "putty-02")
...@@ -317,7 +318,7 @@ If you press on the putty symbol at the left corner of the terminal window, you ...@@ -317,7 +318,7 @@ If you press on the putty symbol at the left corner of the terminal window, you
You can give your session a name so that you can save it and reuse it later. You can give your session a name so that you can save it and reuse it later.
Give you session a name, for example "res-hpc-lo01". **Save** Give you session a name, for example "res-hpc-lo02". **Save**
![alt text](images/putty-09.gif "putty-09") ![alt text](images/putty-09.gif "putty-09")
...@@ -540,7 +541,7 @@ Handy reference: ...@@ -540,7 +541,7 @@ Handy reference:
- ./hello - ./hello
``` ```
Hello world from process 000 out of 001, processor name res-hpc-lo01.researchlumc.nl Hello world from process 000 out of 001, processor name res-hpc-lo02.researchlumc.nl
``` ```
Here you can see that we ran the program only on 1 core of the cpu. (which is the same as running: mpirun -np 1 ./hello) (np = number of processes to launch) Here you can see that we ran the program only on 1 core of the cpu. (which is the same as running: mpirun -np 1 ./hello) (np = number of processes to launch)
...@@ -550,22 +551,22 @@ To make use of the MPI capabilities of the program, we have to run the program w ...@@ -550,22 +551,22 @@ To make use of the MPI capabilities of the program, we have to run the program w
- mpirun ./hello - mpirun ./hello
``` ```
Hello world from process 003 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 003 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 006 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 006 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 013 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 013 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 015 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 015 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 000 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 000 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 005 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 005 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 010 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 010 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 011 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 011 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 012 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 012 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 002 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 002 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 004 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 004 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 007 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 007 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 001 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 001 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 008 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 008 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 009 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 009 out of 016, processor name res-hpc-lo02.researchlumc.nl
Hello world from process 014 out of 016, processor name res-hpc-lo01.researchlumc.nl Hello world from process 014 out of 016, processor name res-hpc-lo02.researchlumc.nl
``` ```
Now the program is using all the cores of the local machine. (which is the same as: mpirun -np 16 ./hello) Now the program is using all the cores of the local machine. (which is the same as: mpirun -np 16 ./hello)
...@@ -622,7 +623,7 @@ The following commands are useful: ...@@ -622,7 +623,7 @@ The following commands are useful:
- sinfo -N -l - sinfo -N -l
``` ```
[user@res-hpc-lo01 ~]$ sinfo [user@res-hpc-lo02 ~]$ sinfo
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
all* up infinite 2 mix res-hpc-exe[014,019] all* up infinite 2 mix res-hpc-exe[014,019]
all* up infinite 1 alloc res-hpc-exe018 all* up infinite 1 alloc res-hpc-exe018
...@@ -630,7 +631,7 @@ all* up infinite 4 idle res-hpc-exe[013,015-017] ...@@ -630,7 +631,7 @@ all* up infinite 4 idle res-hpc-exe[013,015-017]
gpu up infinite 2 mix res-hpc-gpu[01-02] gpu up infinite 2 mix res-hpc-gpu[01-02]
highmem up infinite 1 mix res-hpc-mem01 highmem up infinite 1 mix res-hpc-mem01
[user@res-hpc-lo01 ~]$ sinfo -a [user@res-hpc-lo02 ~]$ sinfo -a
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
all* up infinite 2 mix res-hpc-exe[014,019] all* up infinite 2 mix res-hpc-exe[014,019]
all* up infinite 1 alloc res-hpc-exe018 all* up infinite 1 alloc res-hpc-exe018
...@@ -642,7 +643,7 @@ LKEBgpu up infinite 1 down* res-hpc-lkeb03 ...@@ -642,7 +643,7 @@ LKEBgpu up infinite 1 down* res-hpc-lkeb03
LKEBgpu up infinite 2 mix res-hpc-lkeb[04-05] LKEBgpu up infinite 2 mix res-hpc-lkeb[04-05]
LKEBgpu up infinite 1 idle res-hpc-lkeb01 LKEBgpu up infinite 1 idle res-hpc-lkeb01
[user@res-hpc-lo01 ~]$ sinfo -l [user@res-hpc-lo02 ~]$ sinfo -l
Mon Mar 23 09:21:27 2020 Mon Mar 23 09:21:27 2020
PARTITION AVAIL TIMELIMIT JOB_SIZE ROOT OVERSUBS GROUPS NODES STATE NODELIST PARTITION AVAIL TIMELIMIT JOB_SIZE ROOT OVERSUBS GROUPS NODES STATE NODELIST
all* up infinite 1-infinite no NO all 2 mixed res-hpc-exe[014,019] all* up infinite 1-infinite no NO all 2 mixed res-hpc-exe[014,019]
...@@ -653,7 +654,7 @@ highmem up infinite 1-infinite no NO all 1 mixe ...@@ -653,7 +654,7 @@ highmem up infinite 1-infinite no NO all 1 mixe
``` ```
``` ```
[user@res-hpc-lo01 ~]$ sinfo -l -N -a [user@res-hpc-lo02 ~]$ sinfo -l -N -a
Mon Mar 23 09:34:14 2020 Mon Mar 23 09:34:14 2020
NODELIST NODES PARTITION STATE CPUS S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON NODELIST NODES PARTITION STATE CPUS S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON
res-hpc-exe013 1 all* mixed 16 2:8:1 128800 0 1 (null) none res-hpc-exe013 1 all* mixed 16 2:8:1 128800 0 1 (null) none
...@@ -684,15 +685,15 @@ With the following command, you can get information about your running jobs and ...@@ -684,15 +685,15 @@ With the following command, you can get information about your running jobs and
- squeue -l - squeue -l
``` ```
[user@res-hpc-lo01 mpi-benchmarks]$ squeue [user@res-hpc-lo02 mpi-benchmarks]$ squeue
JOBID PARTITION USER ST TIME NODES NODELIST(REASON) JOBID PARTITION USER ST TIME NODES NODELIST(REASON)
258 all user R 0:03 2 res-hpc-exe[013-014] 258 all user R 0:03 2 res-hpc-exe[013-014]
[user@res-hpc-lo01 mpi-benchmarks]$ squeue -a [user@res-hpc-lo02 mpi-benchmarks]$ squeue -a
JOBID PARTITION USER ST TIME NODES NODELIST(REASON) JOBID PARTITION USER ST TIME NODES NODELIST(REASON)
258 all user R 0:06 2 res-hpc-exe[013-014] 258 all user R 0:06 2 res-hpc-exe[013-014]
[user@res-hpc-lo01 mpi-benchmarks]$ squeue -l [user@res-hpc-lo02 mpi-benchmarks]$ squeue -l
Thu Jan 23 09:14:22 2020 Thu Jan 23 09:14:22 2020
JOBID PARTITION USER STATE TIME TIME_LIMIT NODES NODELIST(REASON) JOBID PARTITION USER STATE TIME TIME_LIMIT NODES NODELIST(REASON)
258 all user RUNNING 0:12 30:00 2 res-hpc-exe[013-014] 258 all user RUNNING 0:12 30:00 2 res-hpc-exe[013-014]
...@@ -716,7 +717,7 @@ An explanation of some state follows: ...@@ -716,7 +717,7 @@ An explanation of some state follows:
With the slurm command **scontrol** you can get a more detailed overview of your running job, node hardware and partitions: With the slurm command **scontrol** you can get a more detailed overview of your running job, node hardware and partitions:
``` ```
[user@res-hpc-lo01 ~]$ scontrol show job 260 [user@res-hpc-lo02 ~]$ scontrol show job 260
JobId=260 JobName=IMB JobId=260 JobName=IMB
UserId=user(225812) GroupId=Domain Users(513) MCS_label=N/A UserId=user(225812) GroupId=Domain Users(513) MCS_label=N/A
Priority=35603 Nice=0 Account=dnst-ict QOS=normal Priority=35603 Nice=0 Account=dnst-ict QOS=normal
...@@ -745,7 +746,7 @@ JobId=260 JobName=IMB ...@@ -745,7 +746,7 @@ JobId=260 JobName=IMB
Power= Power=
MailUser=user@gmail.com MailType=BEGIN,END,FAIL MailUser=user@gmail.com MailType=BEGIN,END,FAIL
[user@res-hpc-lo01 ~]$ scontrol show node res-hpc-exe014 [user@res-hpc-lo02 ~]$ scontrol show node res-hpc-exe014
NodeName=res-hpc-exe014 Arch=x86_64 CoresPerSocket=12 NodeName=res-hpc-exe014 Arch=x86_64 CoresPerSocket=12
CPUAlloc=16 CPUTot=24 CPULoad=0.00 CPUAlloc=16 CPUTot=24 CPULoad=0.00
AvailableFeatures=(null) AvailableFeatures=(null)
...@@ -763,7 +764,7 @@ NodeName=res-hpc-exe014 Arch=x86_64 CoresPerSocket=12 ...@@ -763,7 +764,7 @@ NodeName=res-hpc-exe014 Arch=x86_64 CoresPerSocket=12
CurrentWatts=0 AveWatts=0 CurrentWatts=0 AveWatts=0
ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
[user@res-hpc-lo01 ~]$ scontrol show partition all [user@res-hpc-lo02 ~]$ scontrol show partition all
PartitionName=all PartitionName=all
AllowGroups=ALL AllowAccounts=ALL AllowQos=ALL AllowGroups=ALL AllowAccounts=ALL AllowQos=ALL
AllocNodes=ALL Default=YES QoS=N/A AllocNodes=ALL Default=YES QoS=N/A
...@@ -781,7 +782,7 @@ PartitionName=all ...@@ -781,7 +782,7 @@ PartitionName=all
You can open an interactive session with the **salloc** command: You can open an interactive session with the **salloc** command:
``` ```
[user@res-hpc-lo01 ~]$ salloc -N1 [user@res-hpc-lo02 ~]$ salloc -N1
salloc: Granted job allocation 267 salloc: Granted job allocation 267
salloc: Waiting for resource configuration salloc: Waiting for resource configuration
salloc: Nodes res-hpc-exe013 are ready for job salloc: Nodes res-hpc-exe013 are ready for job
...@@ -793,13 +794,13 @@ salloc: Nodes res-hpc-exe013 are ready for job ...@@ -793,13 +794,13 @@ salloc: Nodes res-hpc-exe013 are ready for job
exit exit
salloc: Relinquishing job allocation 267 salloc: Relinquishing job allocation 267
[user@res-hpc-lo01 ~]$ [user@res-hpc-lo02 ~]$
``` ```
In the example above, we won't run a command so we ended up in the bash environment. In the example above, we won't run a command so we ended up in the bash environment.
With **exit** we leave the environment and we release the node. With **exit** we leave the environment and we release the node.
``` ```
[user@res-hpc-lo01 ~]$ salloc -N1 mpirun ./hello1 [user@res-hpc-lo02 ~]$ salloc -N1 mpirun ./hello1
salloc: Granted job allocation 268 salloc: Granted job allocation 268
salloc: Waiting for resource configuration salloc: Waiting for resource configuration
salloc: Nodes res-hpc-exe013 are ready for job salloc: Nodes res-hpc-exe013 are ready for job
...@@ -811,7 +812,7 @@ Here we allocated 1 node with one core and ran the openmpi compiled "hello1" pro ...@@ -811,7 +812,7 @@ Here we allocated 1 node with one core and ran the openmpi compiled "hello1" pro
Now the same with 2 nodes, 16 cores on each machine: Now the same with 2 nodes, 16 cores on each machine:
``` ```
[user@res-hpc-lo01 ~]$ salloc -N2 --ntasks-per-node=16 mpirun ./hello1 [user@res-hpc-lo02 ~]$ salloc -N2 --ntasks-per-node=16 mpirun ./hello1
salloc: Granted job allocation 270 salloc: Granted job allocation 270
salloc: Waiting for resource configuration salloc: Waiting for resource configuration
salloc: Nodes res-hpc-exe[013-014] are ready for job salloc: Nodes res-hpc-exe[013-014] are ready for job
...@@ -855,13 +856,13 @@ With the **srun** command you can also open an interactive session or you can ru ...@@ -855,13 +856,13 @@ With the **srun** command you can also open an interactive session or you can ru
Interactive: Interactive:
``` ```
[user@res-hpc-lo01 ~]$ srun --pty bash [user@res-hpc-lo02 ~]$ srun --pty bash
[user@res-hpc-exe013 ~]$ exit [user@res-hpc-exe013 ~]$ exit
exit exit
``` ```
Running a program: Running a program:
``` ```
[user@res-hpc-lo01 ~]$ cat hello.sh [user@res-hpc-lo02 ~]$ cat hello.sh
#!/bin/bash #!/bin/bash
# #
...@@ -871,9 +872,9 @@ echo "" ...@@ -871,9 +872,9 @@ echo ""
echo "SLURM_JOB_NAME: $SLURM_JOB_NAME" echo "SLURM_JOB_NAME: $SLURM_JOB_NAME"
echo "SLURM_JOBID: " $SLURM_JOBID echo "SLURM_JOBID: " $SLURM_JOBID
[user@res-hpc-lo01 ~]$ chmod +x hello.sh [user@res-hpc-lo02 ~]$ chmod +x hello.sh
[user@res-hpc-lo01 ~]$ srun -N1 hello.sh [user@res-hpc-lo02 ~]$ srun -N1 hello.sh
Hello from res-hpc-exe013.researchlumc.nl Hello from res-hpc-exe013.researchlumc.nl
It is currently Thu Jan 23 12:35:18 CET 2020 It is currently Thu Jan 23 12:35:18 CET 2020
...@@ -1787,7 +1788,7 @@ You can start to run R interactively, just as an exercise and test. ...@@ -1787,7 +1788,7 @@ You can start to run R interactively, just as an exercise and test.
The recommended way is to run R in batch mode. The recommended way is to run R in batch mode.
``` ```
[username@res-hpc-lo01 ~]$ salloc -N1 -n1 [username@res-hpc-lo02 ~]$ salloc -N1 -n1
salloc: Pending job allocation 386499 salloc: Pending job allocation 386499
salloc: job 386499 queued and waiting for resources salloc: job 386499 queued and waiting for resources
salloc: job 386499 has been allocated resources salloc: job 386499 has been allocated resources
...@@ -1842,7 +1843,7 @@ Rscript --vanilla HelloWorld.R ...@@ -1842,7 +1843,7 @@ Rscript --vanilla HelloWorld.R
Submitted batch job 386860 Submitted batch job 386860
[username@res-hpc-lo01 R]$ cat slurm.out [username@res-hpc-lo02 R]$ cat slurm.out
[1] "Hello world!" [1] "Hello world!"
...@@ -1874,17 +1875,17 @@ Rscript driver.R ...@@ -1874,17 +1875,17 @@ Rscript driver.R
``` ```
``` ```
[username@res-hpc-lo01 R]$ sbatch run.slurm [username@res-hpc-lo02 R]$ sbatch run.slurm
Submitted batch job 386568 Submitted batch job 386568
[username@res-hpc-lo01 R]$ ls -l [username@res-hpc-lo02 R]$ ls -l
total 78 total 78
-rw-r--r-- 1 username Domain Users 59 Jun 5 11:42 driver.R -rw-r--r-- 1 username Domain Users 59 Jun 5 11:42 driver.R
-rw-r--r-- 1 username Domain Users 483 Jun 5 11:42 run.slurm -rw-r--r-- 1 username Domain Users 483 Jun 5 11:42 run.slurm
-rw-r--r-- 1 username Domain Users 0 Jun 5 11:43 slurm.err -rw-r--r-- 1 username Domain Users 0 Jun 5 11:43 slurm.err
-rw-r--r-- 1 username Domain Users 671 Jun 5 11:43 slurm.out -rw-r--r-- 1 username Domain Users 671 Jun 5 11:43 slurm.out
[username@res-hpc-lo01 R]$ cat slurm.out [username@res-hpc-lo02 R]$ cat slurm.out
My sample from N(0,1) is: My sample from N(0,1) is:
[1] 0.32241013 -0.78250675 -0.28872991 0.12559634 -0.29176358 0.57962942 [1] 0.32241013 -0.78250675 -0.28872991 0.12559634 -0.29176358 0.57962942
[7] -0.38277807 -0.21266343 0.86537064 1.06636737 0.96487417 0.31699518 [7] -0.38277807 -0.21266343 0.86537064 1.06636737 0.96487417 0.31699518
...@@ -1898,7 +1899,7 @@ My sample from N(0,1) is: ...@@ -1898,7 +1899,7 @@ My sample from N(0,1) is:
``` ```
``` ```
[username@res-hpc-lo01 R]$ scontrol show job 386568 [username@res-hpc-lo02 R]$ scontrol show job 386568
JobId=386568 JobName=serialR JobId=386568 JobName=serialR
UserId=username(225812) GroupId=Domain Users(513) MCS_label=N/A UserId=username(225812) GroupId=Domain Users(513) MCS_label=N/A
Priority=449759 Nice=0 Account=dnst-ict QOS=normal Priority=449759 Nice=0 Account=dnst-ict QOS=normal
...@@ -1988,7 +1989,7 @@ mpirun Rscript hello.R ...@@ -1988,7 +1989,7 @@ mpirun Rscript hello.R
``` ```
``` ```
[username@res-hpc-lo01 R]$ cat slurm-rmpi.out [username@res-hpc-lo02 R]$ cat slurm-rmpi.out
Hello world from process 000 of 008, on host res-hpc-gpu01 Hello world from process 000 of 008, on host res-hpc-gpu01
Hello world from process 001 of 008, on host res-hpc-gpu01 Hello world from process 001 of 008, on host res-hpc-gpu01
Hello world from process 002 of 008, on host res-hpc-gpu01 Hello world from process 002 of 008, on host res-hpc-gpu01
...@@ -2031,7 +2032,7 @@ rstudio ...@@ -2031,7 +2032,7 @@ rstudio
#### RStudio on a compute node #### RStudio on a compute node
You can also start RStudio on a compute node: You can also start RStudio on a compute node:
``` ```
[username@res-hpc-lo01 ~]$ srun --x11 --pty bash [username@res-hpc-lo02 ~]$ srun --x11 --pty bash
[username@res-hpc-exe014 ~]$ module purge [username@res-hpc-exe014 ~]$ module purge
[username@res-hpc-exe014 ~]$ module add statistical/RStudio/1.3.959/gcc-8.3.1 [username@res-hpc-exe014 ~]$ module add statistical/RStudio/1.3.959/gcc-8.3.1
[username@res-hpc-exe014 ~]$ rstudio [username@res-hpc-exe014 ~]$ rstudio
...@@ -2166,11 +2167,11 @@ Also creating executable in /exports/example/projects/Project-A/bin/python ...@@ -2166,11 +2167,11 @@ Also creating executable in /exports/example/projects/Project-A/bin/python
Installing setuptools, pip, wheel...done. Installing setuptools, pip, wheel...done.
[username@res-hpc-lo01 ~]$ source /exports/example/projects/Project-A/bin/activate [username@res-hpc-lo02 ~]$ source /exports/example/projects/Project-A/bin/activate
(Project-A) [username@res-hpc-lo01 ~]$ (Project-A) [username@res-hpc-lo02 ~]$
(Project-A) [username@res-hpc-lo01 python3.6]$ pip3 list (Project-A) [username@res-hpc-lo02 python3.6]$ pip3 list
Package Version Package Version
---------- ------- ---------- -------
pip 20.1.1 pip 20.1.1
...@@ -2178,8 +2179,8 @@ setuptools 49.1.0 ...@@ -2178,8 +2179,8 @@ setuptools 49.1.0
wheel 0.34.2 wheel 0.34.2
(Project-A) [username@res-hpc-lo01 ~]$ deactivate (Project-A) [username@res-hpc-lo02 ~]$ deactivate
[username@res-hpc-lo01 ~]$ [username@res-hpc-lo02 ~]$
``` ```
To remove your Python virtual environment delete the virtual environment directory. To remove your Python virtual environment delete the virtual environment directory.
...@@ -2313,8 +2314,8 @@ modified /home/username/.bashrc ...@@ -2313,8 +2314,8 @@ modified /home/username/.bashrc
``` ```
``` ```
[username@res-hpc-lo01 ~]$ conda activate Project-B [username@res-hpc-lo02 ~]$ conda activate Project-B
(Project-B) [username@res-hpc-lo01 ~]$ (Project-B) [username@res-hpc-lo02 ~]$
``` ```
``` ```
...@@ -2463,8 +2464,8 @@ Executing transaction: done ...@@ -2463,8 +2464,8 @@ Executing transaction: done
``` ```
``` ```
(Project-B) [username@res-hpc-lo01 ~]$ conda deactivate (Project-B) [username@res-hpc-lo02 ~]$ conda deactivate
[username@res-hpc-lo01 ~]$ [username@res-hpc-lo02 ~]$
``` ```
``` ```
......