For this next use case, a scientist is interested in running a series of metrics over an analysis of interest (the primary entry point for a rperoducible container. He has been given a container with a runscript, and several installed supporting metrics (SCIF apps also in the container), and knows nothing beyond that. You can find the dependency files at https://github.com/sci-f/metrics.scif.
First, clone the repository!
git clone https://github.com/sci-f/metrics.scif
cd metrics.scif
Let’s first build the container. You can use the Makefile to build the image:
make
# Does make clean followed by make build
or manually:
sudo singularity build metrics Singularity
And now run it. This should perform the container’s main function, calling it’s runscript:
./metrics
Hello-World!
Works great! But then what if we wanted to know what tools (SCIF apps) come with the container? That’s easy to do:
./metrics apps
custom
linter
parallel
strace
time
Each of these is suited for a particular use case, discussed next.
A system admin or researcher concerned about evaluation of different software could add relevant metrics apps to the software containers, and then easily evaluate each one with the equivalent command to the container. As an example, here is a simple app to return a table of system traces for some main SCIF app, or a user specific name runscript:
%apprun strace
if [ $# -eq 0 ]
then
exec strace -c -t scif run main
else
exec strace -c -t scif run "$@"
fi
The table returned shows the traces:
$ ./metrics run strace
[strace] executing /bin/bash /scif/apps/strace/scif/runscript
[main] executing /bin/bash /scif/apps/main/scif/runscript
Hello World!
% time seconds usecs/call calls errors syscall
------ ----------- ----------- --------- --------- ----------------
100.00 0.000008 0 40 munmap
0.00 0.000000 0 707 read
0.00 0.000000 0 1 write
0.00 0.000000 0 426 42 open
0.00 0.000000 0 447 close
...
or a set of metrics from “time”
./metrics run time
[time] executing /bin/bash /scif/apps/time/scif/runscript
COMMAND ELAPSED_TIME_HMS AVERAGE_MEM FS_INPUTS MAX_RES_SIZE_KB FS_OUTPUTS PERC_CPU_ALLOCATED CPU_SECONDS_USED W_TIMES_SWAPPED SHARED_TEXT_KB ELAPSED_TIME_SECONDS NUMBER_SIGNALS_DELIVERED AVG_UNSHARED_STACK_SIZE SOCKET_MSG_RECEIVED SOCKET_MSG_SENT AVG_RESIDENT_SET_SIZE CONTEXT_SWITCHES
scif run main 0:00.22 0 74 28120 0 100% 0.21 0 0 0.22 0 0 0 0 0 29
The user can also specify a name of another app in the container to run a system trace for it instead (truncated):
./metrics run strace custom
[strace] executing /bin/bash /scif/apps/strace/scif/runscript custom
[custom] executing /bin/bash /scif/apps/custom/scif/runscript
Beware of a dark-haired man with a loud tie.
(__)
(oo)
/------\/
/ | ||
* /\---/\
~~ ~~
..."Have you mooed today?"...
% time seconds usecs/call calls errors syscall
------ ----------- ----------- --------- --------- ----------------
58.33 0.000014 4 4 wait4
41.67 0.000010 0 426 42 open
0.00 0.000000 0 710 read
0.00 0.000000 0 1 write
0.00 0.000000 0 447 close
...
Regardless of what your runscript does, this app will provide a consistent way to produce this metric. Who knew there were so many open and read calls to just echo-ing a line to the console!
When a container is intended to only perform one function, this use case maps nicely to having a single runscript. As the number of possible functions increase, however, the user is forced to either:
exec command with some known path (to the user)SCI-F apps allow for an easy way to define custom helper metrics or functions for the container. For example, let’s say I created some custom, special metric. Or in this case, it’s more of a container easter egg.
%apprun custom
apt-get moo
and then the resulting output
./metrics run custom
"I wonder", he said to himself, "what's in a book while it's closed. Oh, I
know it's full of letters printed on paper, but all the same, something must
be happening, because as soon as I open it, there's a whole story with people
I don't know yet and all kinds of adventures and battles."
-- Bastian B. Bux
(__)
(oo)
/------\/
/ | ||
* /\---/\
~~ ~~
..."Have you mooed today?"...
This simple ability to create general, modular applications for containers means that we can move toward the possibility that some researchers can specialize in the development of the metrics, and others the analyses.
A SCIF app can be used for general tests that are generalizable to other containers. The example is provided here with the “linter”
./metrics run linter <file>
The app can perform a linting of some default script provided by the container, or a user specified file.
$ ./metrics run linter
[linter] executing /bin/bash /scif/apps/linter/scif/runscript
No config file found, using default configuration
************* Module runscript
E: 1, 0: invalid syntax (<string>, line 1) (syntax-error)
\end{lstlisting}
$ ./metrics run linter script.py
In that a metric can call a runscript, it could be easy to evaluate running the main analysis under various levels or conditions. As a simple proof of concept, here we are creating an app to execute the same exact script in parallel.
%apprun parallel
parallel /bin/bash ::: $SCIF_APPRUN_main $SCIF_APPRUN_main $SCIF_APPRUN_main
./metrics run parallel
[parallel] executing /bin/bash /scif/apps/parallel/scif/runscript
Hello World!
Hello World!
Hello World!
And you might imagine a similar loop to run an analysis, and modify a runtime or system variable for each loop, and save the output (or print to console).
And we don’t need to know anything in advance (paths to hidden executables, how paths or environment should be handled) to run all the container applications, if we wanted to do that. We can use a loop
for app in $(./metrics apps)
do
./metrics run $app
done
This metrics implementation is available for use and documentation provided in entirety on Github. To see (an older) asciicast in its home and original form, you can see it here.
Snakemake and the Scientific Filesystem baa/examples/snakemake.scif
Posted on 30 Jan 2018CarrierSeq: sequence analysis workflow with SCIF baa/examples/carrierseq.scif
Posted on 29 Jan 2018An Introduction to SCI-F Apps baa/examples/tutorials/getting-started
Posted on 29 Jan 2018CarrierSeq: sequence analysis workflow with Singularity + SCIF baa/examples/carrierseq
Posted on 26 Sep 2017Examples (7) Applications (1) Metrics (1) News (1) Tutorials (1)