gprof
Table of Content
Versions and Availability
▶ Display Module Names for gprof on all clusters.
Machine | Version | Module |
---|---|---|
None Available | N/A | N/A |
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
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Shells
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
/bin/bash
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.profile
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.
/bin/tcsh
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
Default Setup
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
The command
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Managing Modules
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
▶ Did not find the version you want to use??
If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.
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Types of request
Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:
- The user's home directory
- Software packages installed here will be accessible only to the user.
- It is suitable for software packages that will be used by a single user.
- Python, Perl and R modules should be installed here.
- /project
- Software packages installed in /project can be accessed by a group of users.
- It is suitable for software packages that
- Need to be shared by users from the same research group, or
- are bigger than the quota on the home file syste.
- This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.
- /usr/local/packages
- Software packages installed under /usr/local/packages can be accessed by all users.
- It is suitable for software packages that will be used by users from multiple research groups.
- This type of request must be sent by the PI of a research group.
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How to request
Please send an email to sys-help@loni.org with the following information:
- Your user name
- The name of cluster where you want to use the requested software
- The name, version and download link of the software
- Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
- Why the software is needed
- Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.
Please note that, once the software is installed, testing and validation are users' responsibility.
About the Software
Description Path: key[@id="gprof"]/whatis Not Found!
Usage
- Use profiling switches when compiling:
-pg
for GNU compilers.
-p -g
for Intel compilers - Execute the program.
- View the output, in file gmon.out, with
gprof
▶ Open Example?
Flat profile: Each sample counts as 0.01 seconds. % cumulative self self total time seconds seconds calls s/call s/call name 56.91 13.33 13.33 11 1.21 1.21 rank 43.16 23.44 10.11 main 0.00 23.44 0.00 2 0.00 0.00 wtime_ 0.00 23.44 0.00 1 0.00 0.00 c_print_results 0.00 23.44 0.00 1 0.00 0.00 timer_clear 0.00 23.44 0.00 1 0.00 0.00 timer_read 0.00 23.44 0.00 1 0.00 0.00 timer_start 0.00 23.44 0.00 1 0.00 0.00 timer_stop % the percentage of the total running time of the time program used by this function. cumulative a running sum of the number of seconds accounted seconds for by this function and those listed above it. self the number of seconds accounted for by this seconds function alone. This is the major sort for this listing. calls the number of times this function was invoked, if this function is profiled, else blank. self the average number of milliseconds spent in this ms/call function per call, if this function is profiled, else blank. total the average number of milliseconds spent in this ms/call function and its descendents per call, if this function is profiled, else blank. name the name of the function. This is the minor sort for this listing. The index shows the location of the function in the gprof listing. If the index is in parenthesis it shows where it would appear in the gprof listing if it were to be printed. Call graph (explanation follows) granularity: each sample hit covers 2 byte(s) for 0.04% of 23.44 seconds index % time self children called name[1] 100.0 10.11 13.33 main [1] 13.33 0.00 11/11 rank [2] 0.00 0.00 1/1 timer_clear [5] 0.00 0.00 1/1 timer_start [7] 0.00 0.00 1/1 timer_read [6] 0.00 0.00 1/1 timer_stop [8] 0.00 0.00 1/1 c_print_results [4] ----------------------------------------------- 13.33 0.00 11/11 main [1] [2] 56.9 13.33 0.00 11 rank [2] ----------------------------------------------- 0.00 0.00 1/2 timer_start [7] 0.00 0.00 1/2 timer_stop [8] [3] 0.0 0.00 0.00 2 wtime_ [3] ----------------------------------------------- 0.00 0.00 1/1 main [1] [4] 0.0 0.00 0.00 1 c_print_results [4] ----------------------------------------------- 0.00 0.00 1/1 main [1] [5] 0.0 0.00 0.00 1 timer_clear [5] ----------------------------------------------- 0.00 0.00 1/1 main [1] [6] 0.0 0.00 0.00 1 timer_read [6] ----------------------------------------------- 0.00 0.00 1/1 main [1] [7] 0.0 0.00 0.00 1 timer_start [7] 0.00 0.00 1/2 wtime_ [3] ----------------------------------------------- 0.00 0.00 1/1 main [1] [8] 0.0 0.00 0.00 1 timer_stop [8] 0.00 0.00 1/2 wtime_ [3] ----------------------------------------------- This table describes the call tree of the program, and was sorted by the total amount of time spent in each function and its children. Each entry in this table consists of several lines. The line with the index number at the left hand margin lists the current function. The lines above it list the functions that called this function, and the lines below it list the functions this one called. This line lists: index A unique number given to each element of the table. Index numbers are sorted numerically. The index number is printed next to every function name so it is easier to look up where the function in the table. % time This is the percentage of the `total' time that was spent in this function and its children. Note that due to different viewpoints, functions excluded by options, etc, these numbers will NOT add up to 100%. self This is the total amount of time spent in this function. children This is the total amount of time propagated into this function by its children. called This is the number of times the function was called. If the function called itself recursively, the number only includes non-recursive calls, and is followed by a `+' and the number of recursive calls. name The name of the current function. The index number is printed after it. If the function is a member of a cycle, the cycle number is printed between the function's name and the index number. For the function's parents, the fields have the following meanings: self This is the amount of time that was propagated directly from the function into this parent. children This is the amount of time that was propagated from the function's children into this parent. called This is the number of times this parent called the function `/' the total number of times the function was called. Recursive calls to the function are not included in the number after the `/'. name This is the name of the parent. The parent's index number is printed after it. If the parent is a member of a cycle, the cycle number is printed between the name and the index number. If the parents of the function cannot be determined, the word ` ' is printed in the `name' field, and all the other fields are blank. For the function's children, the fields have the following meanings: self This is the amount of time that was propagated directly from the child into the function. children This is the amount of time that was propagated from the child's children to the function. called This is the number of times the function called this child `/' the total number of times the child was called. Recursive calls by the child are not listed in the number after the `/'. name This is the name of the child. The child's index number is printed after it. If the child is a member of a cycle, the cycle number is printed between the name and the index number. If there are any cycles (circles) in the call graph, there is an entry for the cycle-as-a-whole. This entry shows who called the cycle (as parents) and the members of the cycle (as children.) The `+' recursive calls entry shows the number of function calls that were internal to the cycle, and the calls entry for each member shows, for that member, how many times it was called from other members of the cycle. Index by function name [4] c_print_results [5] timer_clear [8] timer_stop [1] main [6] timer_read [3] wtime_ [2] rank [7] timer_start
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Last modified: September 10 2020 11:58:50.