In [1]:
!mkdir -p ~/agave/funwave-tvd-docker
%cd ~/agave
!pip3 install setvar
import re
import os
import sys
from setvar import *
from time import sleep
# This cell enables inline plotting in the notebook
%matplotlib inline
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
loadvar()
!auth-tokens-refresh
/home/jovyan/agave
Requirement already satisfied: setvar in /opt/conda/lib/python3.6/site-packages
CMD=jobs-output-get 8979877899256983065-242ac11b-0001-007 fork-command-1.out
INPUTS={"datafile":"agave://nectar-storage-stevenrbrandt/funwave-tvd-docker/rundock.tgz"}
JOB_FILE=job-remote-13262.txt
JOB_ID=8979877899256983065-242ac11b-0001-007
OUTPUT=Successfully submitted job 8979877899256983065-242ac11b-0001-007
REMOTE_COMMAND=tar xzf rundock.tgz && bash rundock.sh
REQUESTBIN_URL=https://requestbin.agaveapi.co/pkxilxpk
STAT=FINISHED
VM_IPADDRESS=18.216.53.253
Token for agave.prod:stevenrbrandt successfully refreshed and cached for 14400 seconds
a283883161e6f7fb10274d6a1921d153
MAINTAINER is a bit of metadata that (hopefully) will allow you to contact the container's creator, if need be.
WORKDIR is the dockerfile equivalent of the "cd" command. Note that running "cd" will not change your directory.
RUN simply runs the command that follows. Because the container is saved after each step, we want to avoid creating files that we don't want to keep (we want containers to be as small as possible).
USER specifies the user id for running subsequent RUN commands.
COPY can be used to copy files into the container from the build directory.
ENTRYPOINT is a script that runs when the container starts up. What our script does is create a new user on the docker image with a user id and name that is convenient.
In [2]:
writefile("funwave-tvd-docker/Dockerfile","""
FROM stevenrbrandt/science-base
USER root
RUN mkdir -p /home/install
RUN chown jovyan /home/install
USER jovyan
MAINTAINER Steven R. Brandt <sbrandt@cct.lsu.edu>
RUN cd /home/install && \
git clone https://github.com/fengyanshi/FUNWAVE-TVD && \
cd FUNWAVE-TVD/src && \
perl -p -i -e 's/FLAG_8 = -DCOUPLING/#$&/' Makefile && \
make
WORKDIR /home/install/FUNWAVE-TVD/src
RUN mkdir -p /home/jovyan/rundir
WORKDIR /home/jovyan/rundir
""")
Writing file `funwave-tvd-docker/Dockerfile'
Now that we've create our Dockerfile and entrypoint.sh, bundle them up in a tarball and send them somewhere that agave can access them.
In [3]:
!tar -czf dockerjob.tgz -C funwave-tvd-docker Dockerfile
!files-mkdir -S ${AGAVE_STORAGE_SYSTEM_ID} -N funwave-tvd-docker
!files-upload -F dockerjob.tgz -S ${AGAVE_STORAGE_SYSTEM_ID} funwave-tvd-docker/
Successfully created folder funwave-tvd-docker
Uploading dockerjob.tgz...
######################################################################## 100.0%
In [4]:
import runagavecmd as r
import imp
imp.reload(r)
Out[4]:
<module 'runagavecmd' from '/home/jovyan/agave/runagavecmd.py'>
Run the docker build command. We will "tag" this build with the name "funwave-tvd" when it is complete.
In [5]:
r.runagavecmd(
"tar xzf dockerjob.tgz && sudo docker build --rm -t funwave-tvd-2 .",
"agave://${AGAVE_STORAGE_SYSTEM_ID}/funwave-tvd-docker/dockerjob.tgz"
)
REMOTE_COMMAND=tar xzf dockerjob.tgz && sudo docker build --rm -t funwave-tvd-2 .
REQUESTBIN_URL=https://requestbin.agaveapi.co/qyc1k8qy
** QUERY STRING FOR REQUESTBIN **
https://requestbin.agaveapi.co/qyc1k8qy?inspect
INPUTS={"datafile":"agave://nectar-storage-stevenrbrandt/funwave-tvd-docker/dockerjob.tgz"}
JOB_FILE=job-remote-19597.txt
Writing file `job-remote-19597.txt'
OUTPUT=Successfully submitted job 4040708458529943065-242ac11b-0001-007
JOB_ID=4040708458529943065-242ac11b-0001-007
STAT=PENDING
STAT=PENDING
STAT=PENDING
STAT=PROCESSING_INPUTS
STAT=STAGING_INPUTS
STAT=STAGED
STAT=STAGED
STAT=SUBMITTING
STAT=SUBMITTING
STAT=SUBMITTING
STAT=FINISHED
CMD=jobs-output-get 4040708458529943065-242ac11b-0001-007 fork-command-1.out
All done! Output follows.
Reading file `fork-command-1.out'
======================================================================
Sending build context to Docker daemon 12.29kB
Step 1/10 : FROM stevenrbrandt/science-base
---> e93db47f971c
Step 2/10 : USER root
---> Using cache
---> b94fc308f479
Step 3/10 : RUN mkdir -p /home/install
---> Using cache
---> beccae742726
Step 4/10 : RUN chown jovyan /home/install
---> Using cache
---> 81c2bd496517
Step 5/10 : USER jovyan
---> Using cache
---> c16d5c774336
Step 6/10 : MAINTAINER Steven R. Brandt <sbrandt@cct.lsu.edu>
---> Using cache
---> f992707e0150
Step 7/10 : RUN cd /home/install && git clone https://github.com/fengyanshi/FUNWAVE-TVD && cd FUNWAVE-TVD/src && perl -p -i -e 's/FLAG_8 = -DCOUPLING/#$&/' Makefile && make
---> Using cache
---> 04bd5f3529fb
Step 8/10 : WORKDIR /home/install/FUNWAVE-TVD/src
---> Using cache
---> 396b8c1fb201
Step 9/10 : RUN mkdir -p /home/jovyan/rundir
---> Using cache
---> 3aecce97d0e7
Step 10/10 : WORKDIR /home/jovyan/rundir
---> Using cache
---> 22beb9c32c31
Successfully built 22beb9c32c31
Successfully tagged funwave-tvd-2:latest
In [6]:
!jobs-output-get ${JOB_ID} fork-command-1.err
!cat fork-command-1.err
Because your docker image has its own internal file system, it can't see files on the host machine. You can, however, transfer them using the "docker cp" command.
Running docker is slightly tricky. When a Docker image starts up, you can execute any command you want--but when you type "exit" all the changes you've made to the file system vanish. Therefore it's necessary to copy them out before the docker container stops.
In [7]:
writefile("rundock.sh","""
rm -fr cid.txt out.tgz
# Start a docker image running in detached mode, write the container id to cid.txt
sudo docker run -d -it --rm --cidfile cid.txt funwave-tvd-2 bash
# Store the container id in CID for convenience
CID=\$(cat cid.txt)
# Copy the input.txt file into the running image
sudo docker cp input.txt \$CID:/home/jovyan/rundir/
# Run funwave on the image
sudo docker exec --user jovyan \$CID mpirun -np 2 /home/install/FUNWAVE-TVD/src/funwave_vessel
# Extract the output files from the running image
# Having them in a tgz makes it more convenient to fetch them with jobs-output-get
sudo docker exec --user jovyan \$CID tar czf - output > out.tgz
# Stop the image
sudo docker stop \$CID
# List the output files
tar tzf out.tgz
""")
Writing file `rundock.sh'
Upload the input.txt file and the rundock.sh script.
In [8]:
!tar czf rundock.tgz rundock.sh input.txt
!files-upload -F rundock.tgz -S ${AGAVE_STORAGE_SYSTEM_ID} funwave-tvd-docker/
Uploading rundock.tgz...
######################################################################## 100.0%
Execute the rundock.sh script
In [9]:
r.runagavecmd(
"tar xzf rundock.tgz && bash rundock.sh",
"agave://${AGAVE_STORAGE_SYSTEM_ID}/funwave-tvd-docker/rundock.tgz")
REMOTE_COMMAND=tar xzf rundock.tgz && bash rundock.sh
REQUESTBIN_URL=https://requestbin.agaveapi.co/1bl4xtf1
** QUERY STRING FOR REQUESTBIN **
https://requestbin.agaveapi.co/1bl4xtf1?inspect
INPUTS={"datafile":"agave://nectar-storage-stevenrbrandt/funwave-tvd-docker/rundock.tgz"}
JOB_FILE=job-remote-19597.txt
Writing file `job-remote-19597.txt'
OUTPUT=Successfully submitted job 799296640238743065-242ac11b-0001-007
JOB_ID=799296640238743065-242ac11b-0001-007
STAT=PENDING
STAT=PENDING
STAT=PENDING
STAT=STAGING_INPUTS
STAT=STAGED
STAT=STAGED
STAT=STAGED
STAT=SUBMITTING
STAT=SUBMITTING
STAT=SUBMITTING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=FINISHED
CMD=jobs-output-get 799296640238743065-242ac11b-0001-007 fork-command-1.out
All done! Output follows.
Reading file `fork-command-1.out'
======================================================================
10a6e2bb73f5dc8718306f090faaebe814345abee91ff763773ab127f4049798
BATHY_CORRECTION DOES NOT EXIST. USE DEFAULT VALUE
INI_UVZ DOES NOT EXIST. USE DEFAULT VALUE
WaterLevel DOES NOT EXIST. USE DEFAULT VALUE
ETA_LIMITER DOES NOT EXIST. USE DEFAULT VALUE
EqualEnergy DOES NOT EXIST. USE DEFAULT VALUE
PERIODIC DOES NOT EXIST. USE DEFAULT VALUE
DIFFUSION_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
DIRECT_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
FRICTION_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
OBSTACLE_FILE DOES NOT EXIST. USE DEFAULT VALUE
BREAKWATER_FILE DOES NOT EXIST. USE DEFAULT VALUE
DISPERSION DOES NOT EXIST. USE DEFAULT VALUE
DISPERSION Default: DISPERSION
Gamma1 DOES NOT EXIST. USE DEFAULT VALUE
Gamma1 Default: 1.0: DISPERSION
Gamma2 DOES NOT EXIST. USE DEFAULT VALUE
Gamma2 Default: 1.0: Full nonlinear
Beta_ref DOES NOT EXIST. USE DEFAULT VALUE
Beta_ref Default: -0.531
Gamma3 DOES NOT EXIST. USE DEFAULT VALUE
Gamma3 Default: 1.0: NOT fully linear
VISCOSITY_BREAKING DOES NOT EXIST. USE DEFAULT VALUE
VISCOSITY_BREAKING Default: SWE Breaking
SWE_ETA_DEP DOES NOT EXIST. USE DEFAULT VALUE
SWE_ETA_DEP Default: 0.8
Friction_Matrix DOES NOT EXIST. USE DEFAULT VALUE
Friction_Matrix Default: constant Cd
Cd DOES NOT EXIST. USE DEFAULT VALUE
Cd_fixed Default: 0.0
Time_Scheme DOES NOT EXIST. USE DEFAULT VALUE
Time_Scheme Default: Runge_Kutta
CONSTRUCTION DOES NOT EXIST. USE DEFAULT VALUE
HIGH_ORDER DOES NOT EXIST. USE DEFAULT VALUE
HIGH_ORDER NOT DEFINED, USE FOURTH-ORDER
CFL DOES NOT EXIST. USE DEFAULT VALUE
CFL Default: 0.5
DT_fixed DOES NOT EXIST. USE DEFAULT VALUE
FroudeCap DOES NOT EXIST. USE DEFAULT VALUE
FroudeCap Default: 3.0
MinDepth DOES NOT EXIST. USE DEFAULT VALUE
MinDepth Default: 0.1 m
MinDepthFrc DOES NOT EXIST. USE DEFAULT VALUE
MinDepthFrc Default: 0.1 m
SHOW_BREAKING DOES NOT EXIST. USE DEFAULT VALUE
SHOW_BREAKING Default: TRUE
Cbrk1 DOES NOT EXIST. USE DEFAULT VALUE
Cbrk1 Default: 0.65
Cbrk2 DOES NOT EXIST. USE DEFAULT VALUE
Cbrk2 Default: 0.35
WAVEMAKER_Cbrk DOES NOT EXIST. USE DEFAULT VALUE
WAVEMAKER_Cbrk Default: 1.0
WAVEMAKER_VIS DOES NOT EXIST. USE DEFAULT VALUE
WAVEMAKER_VIS Default: FALSE
T_INTV_mean DOES NOT EXIST. USE DEFAULT VALUE
T_INTV_mean Default: LARGE
STEADY_TIME DOES NOT EXIST. USE DEFAULT VALUE
STEADY_TIME Default: LARGE
C_smg DOES NOT EXIST. USE DEFAULT VALUE
C_smg Default: 0.0
nu_bkg DOES NOT EXIST. USE DEFAULT VALUE
nu_bkg Default: 0.0
FIELD_IO_TYPE DOES NOT EXIST. USE DEFAULT VALUE
NumberStations DOES NOT EXIST. USE DEFAULT VALUE
OUTPUT_RES DOES NOT EXIST. USE DEFAULT VALUE
OUTPUT_RES NOT FOUND, OUTPUT_RES=1: full resolution
DEPTH_OUT DOES NOT EXIST. USE DEFAULT VALUE
Hmax DOES NOT EXIST. USE DEFAULT VALUE
Hmin DOES NOT EXIST. USE DEFAULT VALUE
Umax DOES NOT EXIST. USE DEFAULT VALUE
MFmax DOES NOT EXIST. USE DEFAULT VALUE
VORmax DOES NOT EXIST. USE DEFAULT VALUE
MASK DOES NOT EXIST. USE DEFAULT VALUE
MASK9 DOES NOT EXIST. USE DEFAULT VALUE
Umean DOES NOT EXIST. USE DEFAULT VALUE
Vmean DOES NOT EXIST. USE DEFAULT VALUE
ETAmean DOES NOT EXIST. USE DEFAULT VALUE
WaveHeight DOES NOT EXIST. USE DEFAULT VALUE
SXL DOES NOT EXIST. USE DEFAULT VALUE
SXR DOES NOT EXIST. USE DEFAULT VALUE
SYL DOES NOT EXIST. USE DEFAULT VALUE
SYR DOES NOT EXIST. USE DEFAULT VALUE
SourceX DOES NOT EXIST. USE DEFAULT VALUE
SourceY DOES NOT EXIST. USE DEFAULT VALUE
P DOES NOT EXIST. USE DEFAULT VALUE
Q DOES NOT EXIST. USE DEFAULT VALUE
Fx DOES NOT EXIST. USE DEFAULT VALUE
Fy DOES NOT EXIST. USE DEFAULT VALUE
Gx DOES NOT EXIST. USE DEFAULT VALUE
Gy DOES NOT EXIST. USE DEFAULT VALUE
AGE DOES NOT EXIST. USE DEFAULT VALUE
OUT_NU DOES NOT EXIST. USE DEFAULT VALUE
TMP DOES NOT EXIST. USE DEFAULT VALUE
EtaBlowVal Default: 100xmax_depth
----------------- STATISTICS ----------------
TIME DT
0.4428E-01 0.4428E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1937E+04 0.1247E+08 0.2996E+01 -0.4596E-06 0.4050E-01 0.4050E-01
MaxTotalU PhaseS Froude
0.4050E-01 0.1066E+02 0.3800E-02
PRINTING FILE NO. 1 TIME/TOTAL: 0.044 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.1017E+01 0.4414E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1927E+04 0.1246E+08 0.1900E+01 -0.1727E-05 0.7329E+00 0.7325E+00
MaxTotalU PhaseS Froude
0.7338E+00 0.1050E+02 0.6987E-01
PRINTING FILE NO. 2 TIME/TOTAL: 1.017 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.2037E+01 0.4473E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1906E+04 0.1246E+08 0.7393E+00 -0.2109E-05 0.9186E+00 0.9148E+00
MaxTotalU PhaseS Froude
0.9215E+00 0.1024E+02 0.8998E-01
PRINTING FILE NO. 3 TIME/TOTAL: 2.037 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.3032E+01 0.4566E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1890E+04 0.1246E+08 0.7188E+00 -0.9413E+00 0.7352E+00 0.6932E+00
MaxTotalU PhaseS Froude
0.7378E+00 0.1019E+02 0.7239E-01
PRINTING FILE NO. 4 TIME/TOTAL: 3.032 / 3.000
Simulation takes 17.199041255997145 seconds
Normal Termination!
10a6e2bb73f5dc8718306f090faaebe814345abee91ff763773ab127f4049798
output/
output/eta_00001
output/v_00003
output/u_00001
output/eta_00003
output/v_00001
output/u_00002
output/eta_00004
output/eta_00002
output/u_00003
output/v_00004
output/v_00002
output/u_00004
Get the output of the job back to our local machine
In [10]:
!jobs-output-list ${JOB_ID}
!jobs-output-get ${JOB_ID} out.tgz
!tar xzf out.tgz
.agave.archive
.agave.log
cid.txt
fork-command-1.err
fork-command-1.ipcexe
fork-command-1.out
fork-command-1.pid
fork-test.txt
fork-wrapper.txt
input.txt
out.tgz
rundock.sh
rundock.tgz
######################################################################## 100.0% 66.2%
In [11]:
!head output/eta_00010
head: cannot open 'output/eta_00010' for reading: No such file or directory
In this first step, we build the singularity installation. Because the result of this job is intended to be an installation for subsequent jobs, we install it to a hard-coded directory rather than using the normal Agave job directory.
In [12]:
!files-mkdir -S ${AGAVE_STORAGE_SYSTEM_ID} -N sing
!files-upload -F input.txt -S ${AGAVE_STORAGE_SYSTEM_ID} sing/
r.runagavecmd(
"mkdir -p ~/singu && "+
"cd ~/singu && "+
"rm -f funwave-tvd.img && "+
"singularity create funwave-tvd.img --size 2000 && "+
"singularity import funwave-tvd.img docker://stevenrbrandt/funwave-tvd-2:latest")
Successfully created folder sing
Uploading input.txt...
######################################################################## 100.0%
REMOTE_COMMAND=mkdir -p ~/singu && cd ~/singu && rm -f funwave-tvd.img && singularity create funwave-tvd.img --size 2000 && singularity import funwave-tvd.img docker://stevenrbrandt/funwave-tvd-2:latest
REQUESTBIN_URL=https://requestbin.agaveapi.co/yj6r3eyj
** QUERY STRING FOR REQUESTBIN **
https://requestbin.agaveapi.co/yj6r3eyj?inspect
INPUTS={}
JOB_FILE=job-remote-19597.txt
Writing file `job-remote-19597.txt'
OUTPUT=Successfully submitted job 4296939754503082471-242ac11b-0001-007
JOB_ID=4296939754503082471-242ac11b-0001-007
STAT=PENDING
STAT=PENDING
STAT=PENDING
STAT=STAGED
STAT=STAGED
STAT=STAGED
STAT=SUBMITTING
STAT=SUBMITTING
STAT=SUBMITTING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
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STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
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STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
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STAT=RUNNING
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STAT=RUNNING
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STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
CMD=jobs-output-get 4296939754503082471-242ac11b-0001-007 fork-command-1.out
All done! Output follows.
Reading file `fork-command-1.out'
======================================================================
Initializing Singularity image subsystem
Opening image file: funwave-tvd.img
Creating 768MiB image
Binding image to loop
Creating file system within image
Image is done: funwave-tvd.img
Docker image path: index.docker.io/stevenrbrandt/funwave-tvd-2:latest
Cache folder set to /home/jovyan/.singularity/docker
[1/13] ||----------------------------------| 0.0%
[1/13] |==|--------------------------------| 7.7%
[2/13] |=====|-----------------------------| 15.4%
[3/13] |========|--------------------------| 23.1%
[4/13] |==========|------------------------| 30.8%
[5/13] |=============|---------------------| 38.5%
[6/13] |================|------------------| 46.2%
[7/13] |==================|----------------| 53.8%
[8/13] |=====================|-------------| 61.5%
[9/13] |========================|----------| 69.2%
[10/13] |==========================|--------| 76.9%
[11/13] |=============================|-----| 84.6%
[12/13] |================================|--| 92.3%
[13/13] |===================================| 100.0%
Importing: base Singularity environment
Importing: /home/jovyan/.singularity/docker/sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:be96bf654103f9670434de9ccc428ee55fb1f14531619dd6cb8fbd85b5765393.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:3f38f85a45654716a81c8ad5c89a0cfc820932422078150624f1f83661b6fec7.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:15bd671928b4d58adb14870cf74c013f9781d4979c944d851827afde27d5bdb8.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:203b799f83cfd0d284472fdd78efc556302c353e270b9974d03cec71a2faf14b.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:c20f403f88792630033b7760769f60fe2da3271d0fdecce4eeeed17c5adfaf21.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:c912233ab5d5939d997ab7a9110bda1f64e2d3cdf3808a21d95736b1da58766f.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:022aa0a604e76c9b9223aa277639f27104b61b6e1c1428ed4174d4c133cd685c.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:630ceed02486a128742ac2b5c3105c88ad28f410a0b2e08ff4ddae2878483924.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:25bb6f291ceb2dcdd3e24aa3a00ef625e6e1a022779283fc2c1b2ccecbc0d162.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:a7cad26d035791e5bf04d6479b03dee59d40a504cfd0b54840966f98b39abfc4.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:f7d512d8250289b154a8e982ff1272ed1376e407bf21f314cd55627c22e5598e.tar.gz
Importing: /home/jovyan/.singularity/docker/sha256:60730f9603637b2b4d71f56eca6b7cf26f3c3a59478c45f1e53733901ea89b02.tar.gz
Now that the Singularity image is built, we can run it with mpi. Notice that mpi executes the singularity command. The tricky part here is to make sure you've got the same version of mpi running inside and outside the container.
In [13]:
!files-upload -F input.txt -S ${AGAVE_STORAGE_SYSTEM_ID} ./
r.runagavecmd(
"export LD_LIBRARY_PATH=/usr/local/lib && "+
"mpirun -np 2 singularity exec ~/singu/funwave-tvd.img /home/install/FUNWAVE-TVD/src/funwave_vessel && "+
"tar cvzf singout.tgz output",
"agave://${AGAVE_STORAGE_SYSTEM_ID}/input.txt"
)
Uploading input.txt...
######################################################################## 100.0%
REMOTE_COMMAND=export LD_LIBRARY_PATH=/usr/local/lib && mpirun -np 2 singularity exec ~/singu/funwave-tvd.img /home/install/FUNWAVE-TVD/src/funwave_vessel && tar cvzf singout.tgz output
REQUESTBIN_URL=https://requestbin.agaveapi.co/17u7mgg1
** QUERY STRING FOR REQUESTBIN **
https://requestbin.agaveapi.co/17u7mgg1?inspect
INPUTS={"datafile":"agave://nectar-storage-stevenrbrandt/input.txt"}
JOB_FILE=job-remote-19597.txt
Writing file `job-remote-19597.txt'
OUTPUT=Successfully submitted job 5360771817640956391-242ac11b-0001-007
JOB_ID=5360771817640956391-242ac11b-0001-007
STAT=PENDING
STAT=PENDING
STAT=PENDING
STAT=PROCESSING_INPUTS
STAT=STAGING_INPUTS
STAT=STAGED
STAT=STAGED
STAT=SUBMITTING
STAT=SUBMITTING
STAT=SUBMITTING
STAT=SUBMITTING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=CLEANING_UP
STAT=FINISHED
CMD=jobs-output-get 5360771817640956391-242ac11b-0001-007 fork-command-1.out
All done! Output follows.
Reading file `fork-command-1.out'
======================================================================
BATHY_CORRECTION DOES NOT EXIST. USE DEFAULT VALUE
INI_UVZ DOES NOT EXIST. USE DEFAULT VALUE
WaterLevel DOES NOT EXIST. USE DEFAULT VALUE
ETA_LIMITER DOES NOT EXIST. USE DEFAULT VALUE
EqualEnergy DOES NOT EXIST. USE DEFAULT VALUE
PERIODIC DOES NOT EXIST. USE DEFAULT VALUE
DIFFUSION_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
DIRECT_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
FRICTION_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
OBSTACLE_FILE DOES NOT EXIST. USE DEFAULT VALUE
BREAKWATER_FILE DOES NOT EXIST. USE DEFAULT VALUE
DISPERSION DOES NOT EXIST. USE DEFAULT VALUE
DISPERSION Default: DISPERSION
Gamma1 DOES NOT EXIST. USE DEFAULT VALUE
Gamma1 Default: 1.0: DISPERSION
Gamma2 DOES NOT EXIST. USE DEFAULT VALUE
Gamma2 Default: 1.0: Full nonlinear
Beta_ref DOES NOT EXIST. USE DEFAULT VALUE
Beta_ref Default: -0.531
Gamma3 DOES NOT EXIST. USE DEFAULT VALUE
Gamma3 Default: 1.0: NOT fully linear
VISCOSITY_BREAKING DOES NOT EXIST. USE DEFAULT VALUE
VISCOSITY_BREAKING Default: SWE Breaking
SWE_ETA_DEP DOES NOT EXIST. USE DEFAULT VALUE
SWE_ETA_DEP Default: 0.8
Friction_Matrix DOES NOT EXIST. USE DEFAULT VALUE
Friction_Matrix Default: constant Cd
Cd DOES NOT EXIST. USE DEFAULT VALUE
Cd_fixed Default: 0.0
Time_Scheme DOES NOT EXIST. USE DEFAULT VALUE
Time_Scheme Default: Runge_Kutta
CONSTRUCTION DOES NOT EXIST. USE DEFAULT VALUE
HIGH_ORDER DOES NOT EXIST. USE DEFAULT VALUE
HIGH_ORDER NOT DEFINED, USE FOURTH-ORDER
CFL DOES NOT EXIST. USE DEFAULT VALUE
CFL Default: 0.5
DT_fixed DOES NOT EXIST. USE DEFAULT VALUE
FroudeCap DOES NOT EXIST. USE DEFAULT VALUE
FroudeCap Default: 3.0
MinDepth DOES NOT EXIST. USE DEFAULT VALUE
MinDepth Default: 0.1 m
MinDepthFrc DOES NOT EXIST. USE DEFAULT VALUE
MinDepthFrc Default: 0.1 m
SHOW_BREAKING DOES NOT EXIST. USE DEFAULT VALUE
SHOW_BREAKING Default: TRUE
Cbrk1 DOES NOT EXIST. USE DEFAULT VALUE
Cbrk1 Default: 0.65
Cbrk2 DOES NOT EXIST. USE DEFAULT VALUE
Cbrk2 Default: 0.35
WAVEMAKER_Cbrk DOES NOT EXIST. USE DEFAULT VALUE
WAVEMAKER_Cbrk Default: 1.0
WAVEMAKER_VIS DOES NOT EXIST. USE DEFAULT VALUE
WAVEMAKER_VIS Default: FALSE
T_INTV_mean DOES NOT EXIST. USE DEFAULT VALUE
T_INTV_mean Default: LARGE
STEADY_TIME DOES NOT EXIST. USE DEFAULT VALUE
STEADY_TIME Default: LARGE
C_smg DOES NOT EXIST. USE DEFAULT VALUE
C_smg Default: 0.0
nu_bkg DOES NOT EXIST. USE DEFAULT VALUE
nu_bkg Default: 0.0
FIELD_IO_TYPE DOES NOT EXIST. USE DEFAULT VALUE
NumberStations DOES NOT EXIST. USE DEFAULT VALUE
OUTPUT_RES DOES NOT EXIST. USE DEFAULT VALUE
OUTPUT_RES NOT FOUND, OUTPUT_RES=1: full resolution
DEPTH_OUT DOES NOT EXIST. USE DEFAULT VALUE
Hmax DOES NOT EXIST. USE DEFAULT VALUE
Hmin DOES NOT EXIST. USE DEFAULT VALUE
Umax DOES NOT EXIST. USE DEFAULT VALUE
MFmax DOES NOT EXIST. USE DEFAULT VALUE
VORmax DOES NOT EXIST. USE DEFAULT VALUE
MASK DOES NOT EXIST. USE DEFAULT VALUE
MASK9 DOES NOT EXIST. USE DEFAULT VALUE
Umean DOES NOT EXIST. USE DEFAULT VALUE
Vmean DOES NOT EXIST. USE DEFAULT VALUE
ETAmean DOES NOT EXIST. USE DEFAULT VALUE
WaveHeight DOES NOT EXIST. USE DEFAULT VALUE
SXL DOES NOT EXIST. USE DEFAULT VALUE
SXR DOES NOT EXIST. USE DEFAULT VALUE
SYL DOES NOT EXIST. USE DEFAULT VALUE
SYR DOES NOT EXIST. USE DEFAULT VALUE
SourceX DOES NOT EXIST. USE DEFAULT VALUE
SourceY DOES NOT EXIST. USE DEFAULT VALUE
P DOES NOT EXIST. USE DEFAULT VALUE
Q DOES NOT EXIST. USE DEFAULT VALUE
Fx DOES NOT EXIST. USE DEFAULT VALUE
Fy DOES NOT EXIST. USE DEFAULT VALUE
Gx DOES NOT EXIST. USE DEFAULT VALUE
Gy DOES NOT EXIST. USE DEFAULT VALUE
AGE DOES NOT EXIST. USE DEFAULT VALUE
OUT_NU DOES NOT EXIST. USE DEFAULT VALUE
TMP DOES NOT EXIST. USE DEFAULT VALUE
EtaBlowVal Default: 100xmax_depth
----------------- STATISTICS ----------------
TIME DT
0.4428E-01 0.4428E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1937E+04 0.1247E+08 0.2996E+01 -0.4596E-06 0.4050E-01 0.4050E-01
MaxTotalU PhaseS Froude
0.4050E-01 0.1066E+02 0.3800E-02
PRINTING FILE NO. 1 TIME/TOTAL: 0.044 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.1017E+01 0.4414E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1927E+04 0.1246E+08 0.1900E+01 -0.1727E-05 0.7329E+00 0.7325E+00
MaxTotalU PhaseS Froude
0.7338E+00 0.1050E+02 0.6987E-01
PRINTING FILE NO. 2 TIME/TOTAL: 1.017 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.2037E+01 0.4473E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1906E+04 0.1246E+08 0.7393E+00 -0.2109E-05 0.9186E+00 0.9148E+00
MaxTotalU PhaseS Froude
0.9215E+00 0.1024E+02 0.8998E-01
PRINTING FILE NO. 3 TIME/TOTAL: 2.037 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.3032E+01 0.4566E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1890E+04 0.1246E+08 0.7188E+00 -0.9413E+00 0.7352E+00 0.6932E+00
MaxTotalU PhaseS Froude
0.7378E+00 0.1019E+02 0.7239E-01
PRINTING FILE NO. 4 TIME/TOTAL: 3.032 / 3.000
Simulation takes 15.861142730995198 seconds
Normal Termination!
output/
output/eta_00001
output/v_00003
output/u_00001
output/eta_00003
output/v_00001
output/u_00002
output/eta_00004
output/eta_00002
output/u_00003
output/v_00004
output/v_00002
output/u_00004
In [14]:
!jobs-output-get ${JOB_ID} singout.tgz
!rm -fr output
!tar xzf singout.tgz
######################################################################## 100.0%
In [20]:
!head output/v_00003
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-0.262768E-06 -0.188281E-06 -0.983997E-07 -0.181027E-07 0.590619E-07 0.169370E-06 0.216881E-06 0.120618E-06 -0.292823E-07 -0.150621E-06 -0.218713E-06 -0.196034E-06 -0.112602E-06 0.404000E-07 0.173452E-06 0.120122E-06 -0.161206E-07 -0.111344E-06 -0.172712E-06 -0.178257E-06 -0.797215E-07 0.428559E-08 0.291667E-07 0.121652E-08 -0.450905E-07 -0.490066E-07 -0.640241E-07 -0.453675E-07 -0.103633E-07 0.400694E-07 0.107394E-06 0.141114E-06 0.104180E-06 -0.376312E-07 -0.158066E-06 -0.196057E-06 -0.108702E-06 -0.136346E-08 0.629010E-07 0.888952E-07 0.198508E-07 -0.963591E-07 -0.179076E-06 -0.221706E-06 -0.196567E-06 -0.133490E-06 -0.237550E-07 0.603392E-07 0.873948E-07 0.175689E-07 -0.729129E-07 -0.387151E-07 0.935526E-07 0.171287E-06 0.810731E-07 -0.726993E-07 -0.214405E-06 -0.229693E-06 -0.130410E-06 -0.593380E-08 0.714865E-07 0.233043E-07 -0.173834E-07 0.157161E-07 0.258325E-07 -0.301636E-07 -0.121584E-06 -0.168509E-06 -0.149967E-06 -0.771106E-07
In this next and final singularity example, we get around the problem of needing to port MPI by using the same MPI that's in the container to launch the containers. The trick is this code, which comes at the end of the .bashrc. What it does is effectively replace our shell on the machine with an execution of bash inside the singularity image.
# Put the full path to a singularity image in the file $HOME/sing.txt.
if [ -r $HOME/work/sing.txt ]
then
IMAGE=$(cat $HOME/work/sing.txt)
fi
if [ "$IMAGE" != "" ]
then
if [ -r "$IMAGE" ]
then
# If the SINGULARITY_CONTAINER variable is set,
# then we are already in the container
if [ "$SINGULARITY_CONTAINER" = "" ]
then
# Switch to running inside singularity
exec singularity exec $IMAGE bash --login
fi
else
echo Could not read image file $IMAGE
fi
fi
In [16]:
!echo /home/jovyan/singu/funwave-tvd.img > ~/work/sing.txt
There's no need to call singularity explicitly, as it's called by each invocation of .bashrc. Note that the funwave-tvd we are executing is the one from inside the image.
In [17]:
!files-upload -F input.txt -S ${AGAVE_STORAGE_SYSTEM_ID} ./
r.runagavecmd(
"rm -fr output && "+
"mpirun -np 2 /home/install/FUNWAVE-TVD/src/funwave_vessel && "+
"tar cvzf singout.tgz output",
"agave://${AGAVE_STORAGE_SYSTEM_ID}/input.txt"
)
Uploading input.txt...
######################################################################## 100.0%
REMOTE_COMMAND=rm -fr output && mpirun -np 2 /home/install/FUNWAVE-TVD/src/funwave_vessel && tar cvzf singout.tgz output
REQUESTBIN_URL=https://requestbin.agaveapi.co/1131s6o1
** QUERY STRING FOR REQUESTBIN **
https://requestbin.agaveapi.co/1131s6o1?inspect
INPUTS={"datafile":"agave://nectar-storage-stevenrbrandt/input.txt"}
JOB_FILE=job-remote-19597.txt
Writing file `job-remote-19597.txt'
OUTPUT=Successfully submitted job 7597476498183155225-242ac11b-0001-007
JOB_ID=7597476498183155225-242ac11b-0001-007
STAT=PENDING
STAT=PENDING
STAT=PENDING
STAT=PROCESSING_INPUTS
STAT=STAGED
STAT=STAGED
STAT=STAGED
STAT=SUBMITTING
STAT=SUBMITTING
STAT=SUBMITTING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=RUNNING
STAT=FINISHED
CMD=jobs-output-get 7597476498183155225-242ac11b-0001-007 fork-command-1.out
All done! Output follows.
Reading file `fork-command-1.out'
======================================================================
BATHY_CORRECTION DOES NOT EXIST. USE DEFAULT VALUE
INI_UVZ DOES NOT EXIST. USE DEFAULT VALUE
WaterLevel DOES NOT EXIST. USE DEFAULT VALUE
ETA_LIMITER DOES NOT EXIST. USE DEFAULT VALUE
EqualEnergy DOES NOT EXIST. USE DEFAULT VALUE
PERIODIC DOES NOT EXIST. USE DEFAULT VALUE
DIFFUSION_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
DIRECT_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
FRICTION_SPONGE DOES NOT EXIST. USE DEFAULT VALUE
OBSTACLE_FILE DOES NOT EXIST. USE DEFAULT VALUE
BREAKWATER_FILE DOES NOT EXIST. USE DEFAULT VALUE
DISPERSION DOES NOT EXIST. USE DEFAULT VALUE
DISPERSION Default: DISPERSION
Gamma1 DOES NOT EXIST. USE DEFAULT VALUE
Gamma1 Default: 1.0: DISPERSION
Gamma2 DOES NOT EXIST. USE DEFAULT VALUE
Gamma2 Default: 1.0: Full nonlinear
Beta_ref DOES NOT EXIST. USE DEFAULT VALUE
Beta_ref Default: -0.531
Gamma3 DOES NOT EXIST. USE DEFAULT VALUE
Gamma3 Default: 1.0: NOT fully linear
VISCOSITY_BREAKING DOES NOT EXIST. USE DEFAULT VALUE
VISCOSITY_BREAKING Default: SWE Breaking
SWE_ETA_DEP DOES NOT EXIST. USE DEFAULT VALUE
SWE_ETA_DEP Default: 0.8
Friction_Matrix DOES NOT EXIST. USE DEFAULT VALUE
Friction_Matrix Default: constant Cd
Cd DOES NOT EXIST. USE DEFAULT VALUE
Cd_fixed Default: 0.0
Time_Scheme DOES NOT EXIST. USE DEFAULT VALUE
Time_Scheme Default: Runge_Kutta
CONSTRUCTION DOES NOT EXIST. USE DEFAULT VALUE
HIGH_ORDER DOES NOT EXIST. USE DEFAULT VALUE
HIGH_ORDER NOT DEFINED, USE FOURTH-ORDER
CFL DOES NOT EXIST. USE DEFAULT VALUE
CFL Default: 0.5
DT_fixed DOES NOT EXIST. USE DEFAULT VALUE
FroudeCap DOES NOT EXIST. USE DEFAULT VALUE
FroudeCap Default: 3.0
MinDepth DOES NOT EXIST. USE DEFAULT VALUE
MinDepth Default: 0.1 m
MinDepthFrc DOES NOT EXIST. USE DEFAULT VALUE
MinDepthFrc Default: 0.1 m
SHOW_BREAKING DOES NOT EXIST. USE DEFAULT VALUE
SHOW_BREAKING Default: TRUE
Cbrk1 DOES NOT EXIST. USE DEFAULT VALUE
Cbrk1 Default: 0.65
Cbrk2 DOES NOT EXIST. USE DEFAULT VALUE
Cbrk2 Default: 0.35
WAVEMAKER_Cbrk DOES NOT EXIST. USE DEFAULT VALUE
WAVEMAKER_Cbrk Default: 1.0
WAVEMAKER_VIS DOES NOT EXIST. USE DEFAULT VALUE
WAVEMAKER_VIS Default: FALSE
T_INTV_mean DOES NOT EXIST. USE DEFAULT VALUE
T_INTV_mean Default: LARGE
STEADY_TIME DOES NOT EXIST. USE DEFAULT VALUE
STEADY_TIME Default: LARGE
C_smg DOES NOT EXIST. USE DEFAULT VALUE
C_smg Default: 0.0
nu_bkg DOES NOT EXIST. USE DEFAULT VALUE
nu_bkg Default: 0.0
FIELD_IO_TYPE DOES NOT EXIST. USE DEFAULT VALUE
NumberStations DOES NOT EXIST. USE DEFAULT VALUE
OUTPUT_RES DOES NOT EXIST. USE DEFAULT VALUE
OUTPUT_RES NOT FOUND, OUTPUT_RES=1: full resolution
DEPTH_OUT DOES NOT EXIST. USE DEFAULT VALUE
Hmax DOES NOT EXIST. USE DEFAULT VALUE
Hmin DOES NOT EXIST. USE DEFAULT VALUE
Umax DOES NOT EXIST. USE DEFAULT VALUE
MFmax DOES NOT EXIST. USE DEFAULT VALUE
VORmax DOES NOT EXIST. USE DEFAULT VALUE
MASK DOES NOT EXIST. USE DEFAULT VALUE
MASK9 DOES NOT EXIST. USE DEFAULT VALUE
Umean DOES NOT EXIST. USE DEFAULT VALUE
Vmean DOES NOT EXIST. USE DEFAULT VALUE
ETAmean DOES NOT EXIST. USE DEFAULT VALUE
WaveHeight DOES NOT EXIST. USE DEFAULT VALUE
SXL DOES NOT EXIST. USE DEFAULT VALUE
SXR DOES NOT EXIST. USE DEFAULT VALUE
SYL DOES NOT EXIST. USE DEFAULT VALUE
SYR DOES NOT EXIST. USE DEFAULT VALUE
SourceX DOES NOT EXIST. USE DEFAULT VALUE
SourceY DOES NOT EXIST. USE DEFAULT VALUE
P DOES NOT EXIST. USE DEFAULT VALUE
Q DOES NOT EXIST. USE DEFAULT VALUE
Fx DOES NOT EXIST. USE DEFAULT VALUE
Fy DOES NOT EXIST. USE DEFAULT VALUE
Gx DOES NOT EXIST. USE DEFAULT VALUE
Gy DOES NOT EXIST. USE DEFAULT VALUE
AGE DOES NOT EXIST. USE DEFAULT VALUE
OUT_NU DOES NOT EXIST. USE DEFAULT VALUE
TMP DOES NOT EXIST. USE DEFAULT VALUE
EtaBlowVal Default: 100xmax_depth
----------------- STATISTICS ----------------
TIME DT
0.4428E-01 0.4428E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1937E+04 0.1247E+08 0.2996E+01 -0.4596E-06 0.4050E-01 0.4050E-01
MaxTotalU PhaseS Froude
0.4050E-01 0.1066E+02 0.3800E-02
PRINTING FILE NO. 1 TIME/TOTAL: 0.044 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.1017E+01 0.4414E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1927E+04 0.1246E+08 0.1900E+01 -0.1727E-05 0.7329E+00 0.7325E+00
MaxTotalU PhaseS Froude
0.7338E+00 0.1050E+02 0.6987E-01
PRINTING FILE NO. 2 TIME/TOTAL: 1.017 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.2037E+01 0.4473E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1906E+04 0.1246E+08 0.7393E+00 -0.2109E-05 0.9186E+00 0.9148E+00
MaxTotalU PhaseS Froude
0.9215E+00 0.1024E+02 0.8998E-01
PRINTING FILE NO. 3 TIME/TOTAL: 2.037 / 3.000
----------------- STATISTICS ----------------
TIME DT
0.3032E+01 0.4566E-01
MassVolume Energy MaxEta MinEta Max U Max V
0.1890E+04 0.1246E+08 0.7188E+00 -0.9413E+00 0.7352E+00 0.6932E+00
MaxTotalU PhaseS Froude
0.7378E+00 0.1019E+02 0.7239E-01
PRINTING FILE NO. 4 TIME/TOTAL: 3.032 / 3.000
Simulation takes 15.642075522999221 seconds
Normal Termination!
output/
output/eta_00001
output/v_00003
output/u_00001
output/eta_00003
output/v_00001
output/u_00002
output/eta_00004
output/eta_00002
output/u_00003
output/v_00004
output/v_00002
output/u_00004
In [18]:
!rm -fr output singout.tgz
!jobs-output-get ${JOB_ID} singout.tgz
!tar xzf singout.tgz
!ls output
######################################################################## 100.0%
eta_00001 eta_00003 u_00001 u_00003 v_00001 v_00003
eta_00002 eta_00004 u_00002 u_00004 v_00002 v_00004
In [19]:
# Clean up so that we don't boot into the singularity image without intending to
!rm -f ~/work/sing.txt
In [ ]:
Content source: agaveapi/SC17-container-tutorial
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