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| software:software [2018-05-08 15:40] – [Availability] frey | software:software [2024-03-26 16:00] – [VALET commands] anita |
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| ====== Availability ====== | ====== Availability ====== |
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| Each cluster has a unique complement of development tools, libraries, and applications. Documentation for all software is organized in alphabetical order on the <wrap hi #2fa4e7>sidebar</wrap> or ''sidebar'' or <wrap em>sidebar</wrap> <html><span style="color: #ffffff; background-color: #2fa4e7; padding: 5px 10px !important; border-radius: 4px;">sidebar</span></html>. | Each cluster has a unique complement of development tools, libraries, and applications. Documentation for all software is organized in alphabetical order on the <html><span style="color:#ffffff;background-color:#2fa4e7;padding:3px 7px !important;border-radius:4px;">sidebar</span></html> |
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| | A list of installed software that IT builds and maintains for each cluster can be found by logging into the cluster (e.g. [[abstract:caviness:system_access:system_access#logging-on-to-caviness|Caviness]] or [[abstract:darwin:system_access:system_access#logging-on-to-darwin|DARWIN]]) and using the VALET command ''vpkg_list''. |
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| | Review the [[http://www.nvidia.com/content/PDF/gpu-accelerated-applications.pdf|nVidia'a GPU-Accelerated Applications list]] for applications optimized to work with GPUs. These applications would be able to take advantage of nodes equipped with nVidia Tesla K20X coprocessors. |
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| | <note important> |
| | Use of some commercial software on the clusters may require that your research group purchase a right-to-use license (e.g. ANSYS, IDL and COMSOL). |
| | </note> |
| ====== Using software ====== | ====== Using software ====== |
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| Preparing the Linux environment for a particular software title usually involves modification of the ''PATH'' or ''LD_LIBRARY_PATH'' variables, setting additional variables in the environment, or even executing scripted commands. Often the documentation for installing such software suggests that the user edit his/her ''.bashrc'' or ''.bash_profile'' file so the changes are made automatically at login. On UD HPC clusters, these tasks are best accomplished using [[:software:valet:01_intro|VALET]], not by editing your login files. | Preparing the Linux environment for a particular software title usually involves modification of the ''PATH'' or ''LD_LIBRARY_PATH'' variables, setting additional variables in the environment, or even executing scripted commands. Often the documentation for installing such software suggests that the user edit his/her ''.bashrc'' or ''.bash_profile'' file so the changes are made automatically at login. On UD HPC clusters, these tasks are best accomplished using [[:software:valet:valet|VALET]], not by editing your login files. |
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| When IT adds new software to a cluster or upgrades existing software titles the work necessary to configure the environment for that software is modeled in a VALET //package file//. Later, when a user issues the ''vpkg_require'' command to prepare his/her environment, VALET uses the package file to affect the necessary changes. | When IT adds new software to a cluster or upgrades existing software titles the work necessary to configure the environment for that software is modeled in a VALET //package file//. Later, when a user issues the ''vpkg_require'' command to prepare his/her environment, VALET uses the package file to affect the necessary changes. |
| The following table provides a brief summary of the most often-used VALET commands. Additional information is available in the [[:software:valet:valet|VALET software documentation]]. These commands are available in login shells and batch scripts (since they are run as login shells). | The following table provides a brief summary of the most often-used VALET commands. Additional information is available in the [[:software:valet:valet|VALET software documentation]]. These commands are available in login shells and batch scripts (since they are run as login shells). |
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| ^Command ^Description ^ | The table below shows the basic informational commands for VALET. In subsequent sections, VALET commands are illustrated in the contexts of application development (e.g., compiling, using libraries) and running IT-installed applications. |
| |''vpkg_list''|List all available //packages// by their <<package-id>>| | |
| |''vpkg_versions'' <<package-id>>|List the versions/variants of a specific package by their <<version-id>>| | ^ Command ^ Function ^ |
| |''vpkg_require'' <<versioned-package-id>>|Attempt to configure the environment to use the given software| | | ''vpkg_help'' | VALET help. | |
| |''vpkg_rollback'' <<number or all>>|Roll back a number of package additions, use all for every package| | | ''vpkg_list'' | List the packages that have VALET configuration files. | |
| | | ''vpkg_versions ''<<//package-id//>> | List versions available for a single package. | |
| | | ''vpkg_info ''<<//package-id//>> | Show information for a single package (or package version). | |
| | | ''vpkg_require ''<<//versioned-package-id//>> | Configure environment for one or more VALET packages. | |
| | | ''vpkg_devrequire ''<<//versioned-package-id//>> | Configure environment for one or more VALET packages including software development variables such as ''CPPFLAGS'' and ''LDFLAGS''. | |
| | | ''vpkg_rollback ''<<//# or all//>> | Each time VALET changes the environment, it makes a snapshot of your environment to which it can return.\\ ''vpkg_rollback'' attempts to restore the UNIX environment to its previous state. You can specify a number (''#'') to revert one or more prior changes to the environment or ''all'' to remove all changes. | |
| | | ''vpkg_history'' | List the versioned packages that have been added to the environment. | |
| | | ''man valet'' | Complete documentation of VALET commands. | |
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| A <<versioned-package-id>> is the combination of a package identifier (found using the ''vpkg_list'' command) with a version/variant identifier (via the ''vpkg_versions'' command). The two pieces are joined using a forward slash (/). For example, the commercial software "Matlab" has a <<package-id>> of ''matlab'' and the 2012 release has a <<version-id>> of ''r2012a'', producing the <<versioned-package-id>> ''matlab/r2012a''. | A <<//versioned-package-id//>> is the combination of a package identifier (found using the ''vpkg_list'' command) with a version/variant identifier (via the ''vpkg_versions'' command). The two pieces are joined using a forward slash (/). For example, the commercial software "Matlab" has a <<//package-id//>> of ''matlab'' and the 2012 release has a <<//version-id//>> of ''r2012a'', producing the <<//versioned-package-id//>> ''matlab/r2012a''. |
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| <note>In the context of a <<versioned-package-id>>, a blank <<version-id>> implies the default version of the package. If the 2012 release of Matlab were the default, then using ''matlab'' (or ''matlab/default'') as the <<versioned-package-id>> would imply ''matlab/r2012a''.</note> | <note>In the context of a <<//versioned-package-id//>>, a blank <<//version-id//>> implies the default version of the package (marked with an asterisk ''*''). If the 2012 release of Matlab were the default, then using ''matlab'' (or ''matlab/default'') as the <<//versioned-package-id//>> would imply ''matlab/r2012a''.</note> |
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| VALET environment changes apply to the shell in which the ''vpkg_require'' command is issued; the changes do not "stick" after exiting that shell (by logging-out, for example). Thus, one way to discard changes affected by a ''vpkg_require'' command is to just exit the shell. The ''vpkg_rollback'' command is a more graceful alternative and iteratively discards the changes produced by prior ''vpkg_require'' commands issued in the shell. To undo all changes, ''vpkg_require all'' can be used. | VALET environment changes apply to the shell in which the ''vpkg_require'' command is issued; the changes do not "stick" after exiting that shell (by logging-out, for example). Thus, one way to discard changes affected by a ''vpkg_require'' command is to just exit the shell. The ''vpkg_rollback'' command is a more graceful alternative and iteratively discards the changes produced by prior ''vpkg_require'' commands issued in the shell. To undo all changes, ''vpkg_require all'' can be used. |