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| abstract:farber:app_dev:compute_env [2018-03-21 16:58] – [Startup and logout scripts] sraskar | abstract:farber:app_dev:compute_env [2021-04-27 16:20] (current) – [Startup and logout scripts] anita |
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| ====== Computing environment ====== | ====== Computing Environment ====== |
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| //This section uses the wiki's [[:#documentation-conventions|documentation conventions]].// | |
| ===== UNIX shell ===== | ===== UNIX shell ===== |
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| The //UNIX shell// is the interface to the UNIX operating system. The HPC cluster allows use of the enhanced Bourne shell //bash//, the enhanced C shell //tcsh//, and the enhanced Korn shell //zsh//. IT will primarily support bash, the default shell. | The //UNIX shell// is the interface to the UNIX operating system. The HPC cluster allows use of the enhanced Bourne shell //bash//, the enhanced C shell //tcsh//, and the enhanced Korn shell //zsh//. IT will primarily support //bash//, the default shell. |
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| For most Linux systems, the //sh// shell is the //bash// shell and the //csh// shell is the //tcsh// shell. The remainder of this document will use only // bash// commands. | For most Linux systems, the //sh// shell is the //bash// shell and the //csh// shell is the //tcsh// shell. The remainder of this document will use only // bash// commands. |
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| | == == |
| | //The following sections use the wiki's [[:#documentation-conventions|documentation conventions]].// |
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| ===== Environment variables ===== | ===== Environment variables ===== |
| <note warning>Spaces are important. Do not put spaces around the equal sign. If the value has spaces, enclose the value in quotes.</note> | <note warning>Spaces are important. Do not put spaces around the equal sign. If the value has spaces, enclose the value in quotes.</note> |
| <note tip>If you see instructions that refer the ''setenv'' command, replace it with the ''export'' **bash** command. Make sure you use equal signs, with no spaces. The ''setenv'' **csh** command uses spaces instead of one equal.</note> | <note tip>If you see instructions that refer the ''setenv'' command, replace it with the ''export'' **bash** command. Make sure you use equal signs, with no spaces. The ''setenv'' **csh** command uses spaces instead of one equal.</note> |
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| ==== Startup and logout scripts ==== | ==== Startup and logout scripts ==== |
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| <code bash> | <code bash> |
| cp /etc/skel/.bash* $HOME | cp /opt/shared/templates/homedir/.bash* $HOME |
| </code> | </code> |
| <note tip>**Where to put startup commands:** You can put bash commands in either ''~/.bashrc'' or ''~/.bash_profile''. Here are general suggestions: | <note tip>**Where to put startup commands:** You can put bash commands in either ''~/.bashrc'' or ''~/.bash_profile''. Here are general suggestions: |
| <note tip> | <note tip> |
| The initialization scripts also set the //standard prompt// with your login name and a shortened host name. | The initialization scripts also set the //standard prompt// with your login name and a shortened host name. |
| For example, if your <<//hostname//>> is ''mills.hpc.udel.edu'' and your <<//login_name//>> is ''traine'', then the //standard prompt// will be | For example, if your <<//hostname//>> is ''farber.hpc.udel.edu'' and your <<//login_name//>> is ''traine'', then the //standard prompt// will be |
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| ''[traine@mills ~]$ '' | ''[traine@farber ~]$ '' |
| </note> | </note> |
| <note important>Clusters may be configured to have multiple login nodes, with one common name for connecting. For example, on the Farber cluster, the hostname may be set to ''login000'' or ''login001'', but the standard prompt and window title bar are set to //farber//. </note> | <note important>Clusters may be configured to have multiple login nodes, with one common name for connecting. For example, on the Farber cluster, the hostname may be set to ''login000'' or ''login001'', but the standard prompt and window title bar are set to //farber//. </note> |
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| ^ Variable ^ Example Value ^ Description ^ | ^ Variable ^ Example Value ^ Description ^ |
| | ''WORKDIR'' | ''/lustre/work/it_css'' \\ or ''/home/work/it_css'' | Group private work directory;\\ dependent on [[:clusters:start|cluster]] filesystems | | | ''WORKDIR'' | ''/home/work/it_css'' | Group private work directory | |
| | ''WORKGROUP'' | ''it_css'' | Current workgroup name | | | ''WORKGROUP'' | ''it_css'' | Current workgroup name | |
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| <note tip>Use ''$WORKDIR'' when you refer to you group private directory. This will improve portability. </note> | <note tip>Use ''$WORKDIR'' when you refer to your group private directory. This will improve portability. </note> |
| <note tip> | <note tip> |
| It is always important to be aware of your current workgroup name. The standard prompt includes the workgroup name, added to your username and host. You must have a workgroup name in your prompt to use that cluster group's (//investing-entity//) compute nodes to submit jobs using [[clusters/mills/runapps?s[]=submit&s[]=job#submitting-jobs-qsub|qsub]] or qlogin. An example prompt after the **workgroup** command, | It is always important to be aware of your current workgroup name. The standard prompt includes the workgroup name, added to your username and host. You must have a workgroup name in your prompt to use that cluster group's (//investing-entity//) compute nodes to submit jobs using [[:abstract:farber:runjobs:schedule_jobs#batch-jobs-qsub|qsub]] or [[:abstract:farber:runjobs:schedule_jobs#interactive-jobs-qlogin|qlogin]]. An example prompt after the **workgroup** command, |
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| ''[(it_css:traine)@mills ~]$ '' | ''[(it_css:traine)@farber ~]$ '' |
| </note> | </note> |
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| It is always important to be aware of your current working directory. The standard prompt ends with the basename of ''PWD''. In these two examples the basename is the same, ''traine'', but the standard bash ''PROMPT_COMMAND'', which is executed every time you change directories, will put the full path of your current working directory in your window title. For example, | It is always important to be aware of your current working directory. The standard prompt ends with the basename of ''PWD''. In these two examples the basename is the same, ''traine'', but the standard bash ''PROMPT_COMMAND'', which is executed every time you change directories, will put the full path of your current working directory in your window title. For example, |
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| ''traine@mills:/lustre/work/it_css/users/traine'' | ''traine@farber:/home/work/it_css/users/traine'' |
| </note> | </note> |
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| </note> | </note> |
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| | //This section uses the wiki's [[:#documentation-conventions|documentation conventions]].// |
| ===== Using VALET and your UNIX environment ===== | ===== Using VALET and your UNIX environment ===== |
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| The UD-developed //VALET// system facilitates your use of compilers, libraries, programming tools and application software. It provides a uniform mechanism for setting up a package's required UNIX environment. VALET is a recursive acronym for **//V//**//ALET //**//A//**//utomates //**//L//**//inux //**//E//**//nvironment //**//T//**//asks//. It provides functionality similar to the **Modules** package used at other HPC sites. | The UD-developed //VALET// system facilitates your use of compilers, libraries, programming tools and application software. It provides a uniform mechanism for setting up a package's required UNIX environment. VALET is a recursive acronym for **//V//**//ALET //**//A//**//utomates //**//L//**//inux //**//E//**//nvironment //**//T//**//asks//. It provides functionality similar to the **Modules** package used at other HPC sites. |
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| VALET commands set the basic environment for software. This may include the ''PATH'', ''MANPATH'', ''INFOPATH'', ''LDPATH'', ''LIBPATH'' and ''LD_LIBRARY_PATH'' environment variables, compiler flags, software directory locations, and license paths. This reduces the need for you to set them or update them yourself when changes are made to system and application software. For example, you might find several versions for a single package name, such as Mathematica/8 and Mathematica/8.0.4. You can even apply VALET commands to packages that you install or alter its actions by customizing VALET's configuration files. Type **man valet** for instructions or see the [[:software:valet:start|VALET software documentation]] for complete details. | VALET commands set the basic environment for software. This may include the ''PATH'', ''MANPATH'', ''INFOPATH'', ''LDPATH'', ''LIBPATH'' and ''LD_LIBRARY_PATH'' environment variables, compiler flags, software directory locations, and license paths. This reduces the need for you to set them or update them yourself when changes are made to system and application software. For example, you might find several versions for a single package name, such as Mathematica/8 and Mathematica/8.0.4. You can even apply VALET commands to packages that you install or alter its actions by customizing VALET's configuration files. Type **man valet** for instructions or see the [[:software:valet:valet|VALET software documentation]] for complete details. |
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| 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. | 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. |