With large :command:`module` setup containing hundreds or even thousands of modulefiles, the processing of commands :subcmd:`module avail<avail>` or :subcmd:`module load<load>`. This is especially the case when all these modulefiles are hosted in a shared filesystem mounted on all nodes of a supercomputer concurrently used by many users.
Such slowness comes from the analysis of the file hierarchy under each enabled modulepath that determines what files are modulefiles, what are the module aliases or symbolic versions set on them, etc. This analysis generates a significant number of I/O operations that linearly grow with the number of modulefiles. Slowness can be more or less observed depending on the underlying storage system and the number of available modulefiles.
This recipe provides examples of the features of Modules that could be leveraged to reduce the I/O load implied by modulepath analysis. It starts with the generation of an example modulefile setup that will be progressively tweaked to observe I/O load reduction.
A general assumption is made here that the more I/O operations there are, the slower the :command:`module` commands could be. So reducing the number of these I/O operations leads to reducing the I/O load.
The strace utility, the Linux syscall tracer, will be used to watch the I/O operations produced by each :command:`module` command run. Examples will focus on the :subcmd:`module avail<avail>` command, which is one of the most I/O intensive and widely utilized by users.
Several features of Modules could be used to reduce the number of I/O operations to analyze the content of modulepath:
- Modules Tcl extension library
- Modulepath rc file
- mcookie_check configuration option
- Virtual modules
- Module cache
Each of the above features contributes to an I/O reduction as described in the following section. Combined use of all these features will give the biggest I/O operation save.
For this recipe, a full modulefile setup has to be generated and it will be progressively modified for the different Modules features that will be used.
2 modulepaths are created with 15 module names in each, each provided in 4 different versions. In one modulepath a :file:`.version` rc file is set for each module name to determine a default version. In the other modulepath a :file:`.modulerc` file is set for each module name to define a symbolic version.
mkdir -p example/reduce-io-load/applications
mkdir -p example/reduce-io-load/libraries
# create dummy application modulefiles
cd example/reduce-io-load/applications
for n in a b c d e f g h i j k l m n o; do
mkdir app$n;
for v in 1.0 2.0 3.0 4.0; do
echo '#%Module' >app$n/$v;
done;
# define default version with .version file
echo '#%Module' >app$n/.version
echo 'set ModulesVersion 2.0' >>app$n/.version
done
cd -
# create dummy library modulefiles
cd example/reduce-io-load/libraries
for n in a b c d e f g h i j k l m n o; do
mkdir lib$n;
for v in 1.0 2.0 3.0 4.0; do
echo '#%Module' >lib$n/$v;
done;
# define symbolic version with .modulerc file
echo -e '#%Module' >lib$n/.modulerc
echo -e "module-version lib$n/3.0 sym" >>lib$n/.modulerc
done
cd -
Some non-modulefile files are added within these modulepaths to simulate documentation files left by mistake in these directories:
touch example/reduce-io-load/applications/appg/README
touch example/reduce-io-load/applications/appl/README
touch example/reduce-io-load/libraries/libg/README
touch example/reduce-io-load/libraries/libl/README
The file permission mode of some modulefiles is set to protect them from being read and simulate a hidden modulefile:
chmod a-r example/reduce-io-load/applications/appg/1.0
chmod a-r example/reduce-io-load/applications/appl/1.0
chmod a-r example/reduce-io-load/libraries/libg/1.0
chmod a-r example/reduce-io-load/libraries/libl/1.0
Additional modulefiles are created with a magic cookie header telling that they are not compatible with the current version of Modules:
echo '#%Module99' >example/reduce-io-load/applications/appg/5.0
echo '#%Module99' >example/reduce-io-load/applications/appl/5.0
echo '#%Module99' >example/reduce-io-load/libraries/libg/5.0
echo '#%Module99' >example/reduce-io-load/libraries/libl/5.0
Once all of the above steps done, we end up with a small scale regular modulefile setup containing 116 modulefiles available to us.
:ps:`$` module purge :ps:`$` export MODULEPATH= :ps:`$` module use example/reduce-io-load/applications :ps:`$` module use example/reduce-io-load/libraries :ps:`$` module -o "" avail -t | wc -l 116
Modules is shipped by default with a Tcl extension library that extends the Tcl language in order to provide more optimized I/O commands to read a file or a directory content than native Tcl commands do.
Compatible with Modules v4.3+
If we rebuild Modules without this library enabled, we will see the benefits of having it enabled:
make distclean
./configure --disable-libtclenvmodules
make modulecmd-test.tcl
chmod +x modulecmd-test.tcl
eval $(tclsh ./modulecmd-test.tcl bash autoinit)
The :command:`strace` tool gives the number and the kind of I/O operations
performed during the module avail
command:
:ps:`$` strace -f -c -S name -e trace=%file,%desc -U calls,errors,name \ --silence=attach $MODULES_CMD bash avail 2>no_extlib.out
Once this first stat output is obtained, rebuild Modules with Tcl extension library enabled and fetch :command:`icdiff` tool to compare results.
make distclean
./configure --enable-libtclenvmodules
make modulecmd-test.tcl lib/libtclenvmodules.so
chmod +x modulecmd-test.tcl
make icdiff
Then collect stats and compare results obtained:
:ps:`$` strace -f -c -S name -e trace=%file,%desc -U calls,errors,name \ --silence=attach $MODULES_CMD bash avail 2>with_extlib.out :ps:`$` ./icdiff --cols=76 no_extlib.out with_extlib.out :sgrhi:`no_extlib.out` :sgrhi:`with_extlib.out` calls errors syscall calls errors syscall --------- --------- ---------------- --------- --------- ---------------- :sgrb:`36` 2 access :sgra:`37` 2 access :sgrb:`248` close :sgra:`217` close 2 dup2 2 dup2 8 6 execve 8 6 execve :sgrb:`166` :sgrhi:`fcntl` :sgra:`12` :sgrhi:`fcntl` :sgrb:`1` getcwd :sgra:`2` getcwd :sgrb:`128` :sgrhi:`getdents64` :sgra:`64` :sgrhi:`getdents64` :sgrb:`166 161` :sgrhi:`ioctl` :sgra:`12 7` :sgrhi:`ioctl` 9 4 lseek 9 4 lseek :sgrb:`50` mmap :sgra:`54` mmap :sgrb:`86` newfstatat :sgra:`55` newfstatat :sgrb:`250` 10 openat :sgra:`219` 10 openat 2 pipe 2 pipe 10 pread64 10 pread64 :sgrb:`354` read :sgra:`355` read :sgrb:`1452 1452` :sgrhi:`readlink` :sgra:`25 25` :sgrhi:`readlink` :sgrb:`354` 2 :sgrhi:`stat` :sgra:`196` 2 :sgrhi:`stat` 1 unlink 1 unlink 20 write 20 write --------- --------- ---------------- --------- --------- ---------------- :sgrb:`3335 1637` :sgrhi:`total` :sgra:`1292 56` :sgrhi:`total`
Modules Tcl extension library greatly reduces the number of filesystem I/O
operations by removing unneeded ioctl
, fcntl
and readlink
system
calls done (by Tcl open
command) to read each file. Directory content read
is also improved by fetching hidden and regular files in one pass, which
divides by 2 the number of getdents
call. stat
calls are also reduced
as files found in directories are not checked prior attempting to opening
them.
A .modulerc
file found at the root of an enabled modulepath directory is
now evaluated when modulepath is walked through to locate modulefiles. This
file could hold the rc definition of the whole modules located in the
modulepath, instead of having specific .modulerc
or .version
file for
each module directory within the modulepath.
Compatible with Modules v4.3+
Let's migrate the .modulerc
definition under each module directory in the
.modulerc
file at the root of the modulepath directory. And also translate
the content of .version
files in :mfcmd:`module-version` commands that
could be stored in this top-level rc file. Then all the .modulerc
and
.version
files under module directories are deleted to only keep one
.modulerc
per modulepath.
cd example/reduce-io-load/applications
echo '#%Module' >.modulerc
for n in *; do
v=$(grep set $n/.version | cut -d ' ' -f 3);
echo "module-version $n/$v default" >>.modulerc;
rm -f $n/.version
done
cd -
cd example/reduce-io-load/libraries
echo '#%Module' >.modulerc
for n in *; do
grep module-version $n/.modulerc >>.modulerc;
rm -f $n/.modulerc
done
cd -
Once this change on the module trees has been done, collect new statistics and compare them to those generated previously.
:ps:`$` strace -f -c -S name -e trace=%file,%desc -U calls,errors,name \ --silence=attach $MODULES_CMD bash avail 2>with_modulepath_rc.out :ps:`$` ./icdiff --cols=76 with_extlib.out with_modulepath_rc.out :sgrhi:`with_extlib.out` :sgrhi:`with_modulepath_rc.out` calls errors syscall calls errors syscall --------- --------- ---------------- --------- --------- ---------------- :sgrb:`37` 2 :sgrhi:`access` :sgra:`9` 2 :sgrhi:`access` :sgrb:`217` :sgrhi:`close` :sgra:`189` :sgrhi:`close` 2 dup2 2 dup2 8 6 execve 8 6 execve 12 fcntl 12 fcntl 2 getcwd 2 getcwd 64 getdents64 64 getdents64 12 7 ioctl 12 7 ioctl 9 4 lseek 9 4 lseek 54 mmap 54 mmap 55 newfstatat 55 newfstatat :sgrb:`219` 10 :sgrhi:`openat` :sgra:`191` 10 :sgrhi:`openat` 2 pipe 2 pipe 10 pread64 10 pread64 :sgrb:`355` :sgrhi:`read` :sgra:`299` :sgrhi:`read` 25 25 readlink 25 25 readlink :sgrb:`196` 2 :sgrhi:`stat` :sgra:`168` 2 :sgrhi:`stat` 1 unlink 1 unlink 12 write 12 write --------- --------- ---------------- --------- --------- ---------------- :sgrb:`1292` 56 :sgrhi:`total` :sgra:`1124` 56 :sgrhi:`total`
With this change we have saved the access
, stat
, open
, read
and close
calls needed to analyze the 15 .modulerc
and 15 .version
files that have been removed and replaced by 2 top-level .modulerc
files.
A new configuration option named :mconfig:`mcookie_check` has been introduced
to control the verification made to files to determine if they are
modulefiles. By default this configuration option is set to always
and
when searching for modulefiles within enabled modulepaths each file below
these directories is opened to check if it starts with the Modules magic
cookie (i.e., #%Module
file signature).
These historical checks lead to a large number of I/O operations but if the
option is set to the eval
value, files are not checked anymore when
searching for modulefiles, only when evaluating them.
Compatible with Modules v5.1+
Here we are setting the :mconfig:`mcookie_check` configuration to the eval
value to skip all test on files hosted in modulepath directories and see what
happens when listing available modulefiles:
:ps:`$` module config mcookie_check eval :ps:`$` module -o "" avail -t | wc -l 128 :ps:`$` module avail -o "" appg appl libg libl appg/1.0 appg/2.0 appg/3.0 appg/4.0 appg/5.0 appg/README appl/1.0 appl/2.0 appl/3.0 appl/4.0 appl/5.0 appl/README libg/1.0 libg/2.0 libg/3.0(sym) libg/4.0 libg/5.0 libg/README libl/1.0 libl/2.0 libl/3.0(sym) libl/4.0 libl/5.0 libl/README
12 more modulefiles are returned. Indeed the file checks done by default are useful but we could disable them if a special care is given to the content of modulepath directories. First, we have to eliminate the non-modulefiles stored in these directories:
rm -f example/reduce-io-load/applications/appg/README
rm -f example/reduce-io-load/applications/appl/README
rm -f example/reduce-io-load/libraries/libg/README
rm -f example/reduce-io-load/libraries/libl/README
Then a :mfcmd:`module-hide` command in modulepath's .modulerc
file should
be added for each the modulefile that is read-protected through the use of
file permission modes. This way :command:`module` will know that modulefile is
hidden.
cd example/reduce-io-load/applications
echo 'module-hide --hard appg/1.0' >>.modulerc
echo 'module-hide --hard appl/1.0' >>.modulerc
cd -
cd example/reduce-io-load/libraries
echo 'module-hide --hard libg/1.0' >>.modulerc
echo 'module-hide --hard libl/1.0' >>.modulerc
cd -
A :mfcmd:`module-hide` command in modulepath's .modulerc
file should also
be defined for each modulefile requiring a specific Modules version in its
magic cookie. :command:`module` will skip such modulefiles in case its version
is not compatible with them.
cd example/reduce-io-load/applications
echo 'if {$ModuleToolVersion < 99} {' >>.modulerc
echo ' module-hide --hard appg/5.0' >>.modulerc
echo ' module-hide --hard appl/5.0' >>.modulerc
echo '}' >>.modulerc
cd -
cd example/reduce-io-load/libraries
echo 'if {$ModuleToolVersion < 99} {' >>.modulerc
echo ' module-hide --hard libg/5.0' >>.modulerc
echo ' module-hide --hard libl/5.0' >>.modulerc
echo '}' >>.modulerc
cd -
Once this specific setup has been achieved to get in full control of the content of each modulepaths, we get the accurate listing result with the eval mode of :mconfig:`mcookie_check`.
:ps:`$` module -o "" avail -t | wc -l 116 :ps:`$` strace -f -c -S name -e trace=%file,%desc -U calls,errors,name \ --silence=attach $MODULES_CMD bash avail 2>mcookie_check_eval.out :ps:`$` ./icdiff --cols=76 with_modulepath_rc.out mcookie_check_eval.out :sgrhi:`with_modulepath_rc.out` :sgrhi:`mcookie_check_eval.out` calls errors syscall calls errors syscall --------- --------- ---------------- --------- --------- ---------------- 9 2 access 9 2 access :sgrb:`189` :sgrhi:`close` :sgra:`65` :sgrhi:`close` 2 dup2 2 dup2 8 6 execve 8 6 execve 12 fcntl 12 fcntl 2 getcwd 2 getcwd 64 getdents64 64 getdents64 12 7 ioctl 12 7 ioctl 9 4 lseek 9 4 lseek 54 mmap 54 mmap 55 newfstatat 55 newfstatat :sgrb:`191 10` :sgrhi:`openat` :sgra:`63` 6 :sgrhi:`openat` 2 pipe 2 pipe 10 pread64 10 pread64 :sgrb:`299` :sgrhi:`read` :sgra:`175` :sgrhi:`read` 25 25 readlink 25 25 readlink :sgrb:`168` 2 stat :sgra:`164` 2 stat 1 unlink 1 unlink 12 write 12 write --------- --------- ---------------- --------- --------- ---------------- :sgrb:`1124 56` :sgrhi:`total` :sgra:`744 52` :sgrhi:`total`
A significant drop in I/O calls can be observed from this finely tuned setup.
open
, read
and close
calls are saved for the 4 non-modulefiles
deleted, the 8 modulefiles made hidden and of course for the 116 regular
modulefiles available. As demonstrated, such gain requires a complete control
over the modulepath content and specific care for unsupported or
read-protected files.
A virtual module stands for a module name associated to a modulefile. Instead
of looking for files under modulepaths to get modulefiles, a virtual module
is defined in .modulerc
file with the :mfcmd:`module-virtual` modulefile
command which saves walk down I/O operations to analyze modulepath directory
content.
Compatible with Modules v4.1+
Let's create 2 new modulepaths that will only contain a .modulerc
file in
which a virtual module is defined for each existing modulefile in initial
modulepath. Content of the .modulerc
in the initial modulepaths is also
copied in the .modulerc
of the virtual modulepaths.
mkdir example/reduce-io-load/applications-virt
mkdir example/reduce-io-load/libraries-virt
cd example/reduce-io-load/applications
echo '#%Module' >../applications-virt/.modulerc
for mod in */*; do
echo "module-virtual $mod ../applications/$mod" \
>>../applications-virt/.modulerc;
done
grep -v '#%Module' .modulerc >>../applications-virt/.modulerc
cd -
cd example/reduce-io-load/libraries
echo '#%Module' >../libraries-virt/.modulerc
for mod in */*; do
echo "module-virtual $mod ../libraries/$mod" \
>>../libraries-virt/.modulerc;
done
grep -v '#%Module' .modulerc >>../libraries-virt/.modulerc
cd -
Once the setup of the virtual modulepaths is finished, the environment of the :command:`module` command has to be changed to use these new modulepaths instead of the original ones.
:ps:`$` module unuse example/reduce-io-load/applications :ps:`$` module unuse example/reduce-io-load/libraries :ps:`$` module use example/reduce-io-load/applications-virt :ps:`$` module use example/reduce-io-load/libraries-virt
Then we can check we obtain the same output as with the original setup, 116 modulefiles available. After that collect I/O operation statistics and compare them to those previously fetched.
:ps:`$` module -o "" avail -t | wc -l 116 :ps:`$` strace -f -c -S name -e trace=%file,%desc -U calls,errors,name \ --silence=attach $MODULES_CMD bash avail 2>with_virtual_modules.out :ps:`$` ./icdiff --cols=76 mcookie_check_eval.out with_virtual_modules.out :sgrhi:`mcookie_check_eval.out` :sgrhi:`with_virtual_modules.out` ... calls errors syscall calls errors syscall --------- --------- ---------------- --------- --------- ---------------- 9 2 access 9 2 access :sgrb:`65` :sgrhi:`close` :sgra:`35` :sgrhi:`close` 2 dup2 2 dup2 8 6 execve 8 6 execve 12 fcntl 12 fcntl 2 getcwd 2 getcwd :sgrb:`64` :sgrhi:`getdents64` :sgra:`4` :sgrhi:`getdents64` 12 7 ioctl 12 7 ioctl 9 4 lseek 9 4 lseek 54 mmap 54 mmap :sgrb:`55` :sgrhi:`newfstatat` :sgra:`25` :sgrhi:`newfstatat` :sgrb:`63` 6 :sgrhi:`openat` :sgra:`33` 6 :sgrhi:`openat` 2 pipe 2 pipe 10 pread64 10 pread64 175 read 175 read 25 25 readlink 25 25 readlink :sgrb:`164` 2 :sgrhi:`stat` :sgra:`10` 2 :sgrhi:`stat` 1 unlink 1 unlink 12 write 12 write --------- --------- ---------------- --------- --------- ---------------- :sgrb:`744` 52 :sgrhi:`total` :sgra:`440` 52 :sgrhi:`total`
A large I/O operation drop is observed with the virtual modulepath setup.
The analysis of the 15 module directories under each of the 2 original
modulepaths is not anymore needed as the .modulerc
in the 2 virtual
modulepaths already point to the modulefile location. stat
, open
,
getdents
and close
I/O calls are saved due to that.
Module cache can be built for every modulepaths with :subcmd:`cachebuild` sub-command. When a cache file is found for an enabled modulepath, this file is evaluated instead of walking down the content of the modulepath directory.
Compatible with Modules v5.3+
Here we start over the module setup at the end of the Modulepath rc file section, restoring :mconfig:`mcookie_check` configuration to default, building cache and setting cache read buffer to maximum value.
:ps:`$` module unuse example/reduce-io-load/applications-virt :ps:`$` module unuse example/reduce-io-load/libraries-virt :ps:`$` module use example/reduce-io-load/applications :ps:`$` module use example/reduce-io-load/libraries :ps:`$` module config mcookie_check always :ps:`$` module cachebuild Creating :sgrhi:`example/reduce-io-load/libraries/.modulecache` Creating :sgrhi:`example/reduce-io-load/applications/.modulecache` :ps:`$` module config cache_buffer_bytes 1000000
Once things are setup, new statistics are collected and compared between when cache is used or when it is ignored.
:ps:`$` module -o "" avail -t | wc -l 116 :ps:`$` strace -f -c -S name -e trace=%file,%desc -U calls,errors,name \ --silence=attach $MODULES_CMD bash avail 2>with_cache.out :ps:`$` strace -f -c -S name -e trace=%file,%desc -U calls,errors,name \ --silence=attach $MODULES_CMD bash avail --ignore-cache 2>no_cache.out :ps:`$` ./icdiff --cols=76 no_cache.out with_cache.out :sgrhi:`no_cache.out` :sgrhi:`with_cache.out` calls errors syscall calls errors syscall --------- --------- ---------------- --------- --------- ---------------- :sgrb:`9` 2 access :sgra:`10` 2 access :sgrb:`183` :sgrhi:`close` :sgra:`29` :sgrhi:`close` 2 dup2 2 dup2 9 7 execve 9 7 execve :sgrb:`12` fcntl :sgra:`15` fcntl 1 getcwd 1 getcwd :sgrb:`64` :sgrhi:`getdents64` :sgrb:`12 7` ioctl :sgra:`15 10` ioctl :sgrb:`9` 4 lseek :sgra:`10` 4 lseek :sgrb:`37` mmap :sgra:`38` mmap :sgrb:`221` 2 :sgrhi:`newfstatat` :sgra:`30` 2 :sgrhi:`newfstatat` :sgrb:`187` 10 :sgrhi:`openat` :sgra:`33` 10 :sgrhi:`openat` 2 pipe2 2 pipe2 10 pread64 10 pread64 :sgrb:`324` :sgrhi:`read` :sgra:`209` :sgrhi:`read` :sgrb:`35 35` readlink :sgra:`54 54` readlink 1 unlink 1 unlink 12 write 12 write --------- --------- ---------------- --------- --------- ---------------- :sgrb:`1130 67` :sgrhi:`total` :sgra:`480 89` :sgrhi:`total`
When a cache is found, one file is read instead of checking all directories and files in modulepath directory. Only the modulefiles and directories that are not accessible for everyone are live checked after reading cache file to see if these elements are available to current user.
It explains the significant I/O call drop that can be observed here. Some I/O calls are slightly higher due to the evaluation of module cache files.
Combining all the 4 first features or last one detailed above leads to a significant drop in I/O operations. Almost all remaining I/O calls are made for the initialization of the :command:`module` command run.
It is advised to run this recipe code on your setup to observe the I/O load gain you could obtain. As said earlier the less I/O operations there are, the faster the :command:`module` command could be. But this highly depends on your storage system, on the number of modulefiles and on the number of active users. You may not notice a big difference if your modulefiles are installed on a local SSD storage whereas it can be a game changer if instead the modulefiles are hosted on a shared HDD filesystem that is accessed by hundreds of users.