Code Compilation on the teaching cluster - Revision history

Moses at 14:55, 6 September 2023

2023-09-06T14:55:59Z

← Older revision		Revision as of 10:55, 6 September 2023
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	Sample partial output of this command:		Sample partial output of this command:
	<pre class="gcomment">		<pre class="gcomment">
	[shtsai@d2-13 ~]$ module spider GCC		[shtsai@rb1-11 ~]$ module spider GCC
	-----------------------------------------------------------------------------------------------------------------		-----------------------------------------------------------------------------------------------------------------
	GCC:		GCC:
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	Sample output of this command		Sample output of this command
	<pre class="gcomment">		<pre class="gcomment">
	[shtsai@d2-13 ~]$ ml spider intel-compilers		[shtsai@rb1-11 ~]$ ml spider intel-compilers

	-----------------------------------------------------------------------------------------------------------------		-----------------------------------------------------------------------------------------------------------------
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	Sample output of this command		Sample output of this command
	<pre class="gcomment">		<pre class="gcomment">
	[shtsai@d2-13 ~]$ module spider LLVM		[shtsai@rb1-11 ~]$ module spider LLVM
	------------------------------------------------------------------------------------------------------------------------------------		------------------------------------------------------------------------------------------------------------------------------------
	LLVM:		LLVM:
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	When you load a foss toolchain, all it components will be loaded. For example:		When you load a foss toolchain, all it components will be loaded. For example:
	<pre class="gcommand">		<pre class="gcommand">
	[shtsai@d2-13 ~]$ module list		[shtsai@rb1-11 ~]$ module list
	No modules loaded		No modules loaded
	[shtsai@d2-13 ~]$ module load foss/2022a		[shtsai@rb1-11 ~]$ module load foss/2022a
	[shtsai@d2-13 ~]$ module list		[shtsai@rb1-11 ~]$ module list

	Currently Loaded Modules:		Currently Loaded Modules:
Line 303:		Line 303:
	When you load an intel toolchain, all it components will be loaded. For example:		When you load an intel toolchain, all it components will be loaded. For example:
	<pre class="gcommand">		<pre class="gcommand">
	[shtsai@d2-13 ~]$ module list		[shtsai@rb1-11 ~]$ module list
	No modules loaded		No modules loaded
	[shtsai@d2-13 ~]$ module load intel/2022a		[shtsai@rb1-11 ~]$ module load intel/2022a
	[shtsai@d2-13 ~]$ module list		[shtsai@rb1-11 ~]$ module list

	Currently Loaded Modules:		Currently Loaded Modules:
Line 401:		Line 401:

	<pre class="gcommand">		<pre class="gcommand">
	[shtsai@d2-13 ~]$ module list		[shtsai@rb1-11 ~]$ module list
	No modules loaded		No modules loaded
	[shtsai@d2-13 ~]$ module load GCC/11.3.0		[shtsai@rb1-11 ~]$ module load GCC/11.3.0
	[shtsai@d2-13 ~]$ echo $EBROOTGCC		[shtsai@rb1-11 ~]$ echo $EBROOTGCC
	/apps/eb/GCCcore/11.3.0		/apps/eb/GCCcore/11.3.0
	[shtsai@d2-13 ~]$ echo $EBROOTGSL		[shtsai@rb1-11 ~]$ echo $EBROOTGSL

	[shtsai@d2-13 ~]$ module load GSL/2.7-GCC-11.3.0		[shtsai@rb1-11 ~]$ module load GSL/2.7-GCC-11.3.0
	[shtsai@d2-13 ~]$ echo $EBROOTGSL		[shtsai@rb1-11 ~]$ echo $EBROOTGSL
	/apps/eb/GSL/2.7-GCC-11.3.0		/apps/eb/GSL/2.7-GCC-11.3.0
	[shtsai@d2-13 ~]$		[shtsai@rb1-11 ~]$
	</pre>		</pre>

Moses at 14:50, 6 September 2023

2023-09-06T14:50:55Z

← Older revision		Revision as of 10:50, 6 September 2023
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	</pre>		</pre>

	For detailed information on how to access the compute node interactively for code compilation, please see [[Running Jobs on ~~Sapelo2~~]].		For detailed information on how to access the compute node interactively for code compilation, please see [[Running Jobs on the teaching cluster]].

	----		----

Moses at 14:50, 6 September 2023

2023-09-06T14:50:05Z

← Older revision		Revision as of 10:50, 6 September 2023
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	Code compilation can be done in an interactive session. To start an interactive session, first login into ~~Sapelo2~~ and from there issue the <code>interact</code> command		Code compilation can be done in an interactive session. To start an interactive session, first login into the teaching cluster and from there issue the <code>interact</code> command
	<pre class="gcommand">		<pre class="gcommand">
	interact		interact
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	==Compilers==		==Compilers==

	A number of Fortran and C/C++ compilers, as well as Java and scripting languages such as Perl and Python, are available on ~~Sapelo2~~.		A number of Fortran and C/C++ compilers, as well as Java and scripting languages such as Perl and Python, are available on the teaching cluster.

	=== Summary of main Fortran and C/C++ compilers installed ===		=== Summary of main Fortran and C/C++ compilers installed ===
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	=== Some commonly used compiler options ===		=== Some commonly used compiler options ===

	==== PGI compiler suite (To be added on ~~Sapelo2~~)====		==== PGI compiler suite (To be added on the teaching cluster)====
	{\| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"		{\| class="wikitable unsortable" width="100%" border="1" cellspacing="0" cellpadding="2" align="center"
	\|-		\|-
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	== Compiler Toolchains==		== Compiler Toolchains==
	On ~~Sapelo2~~ we use the [https://easybuild.readthedocs.io/en/latest/ EasyBuild] framework to install software applications. The EasyBuild toolchains are also available for users to compile their own code. Each toolchain provides a compiler suite and some basic libraries, such as MPI, BLAS, LAPACK, FFTW, etc.		On the teaching cluster we use the [https://easybuild.readthedocs.io/en/latest/ EasyBuild] framework to install software applications. The EasyBuild toolchains are also available for users to compile their own code. Each toolchain provides a compiler suite and some basic libraries, such as MPI, BLAS, LAPACK, FFTW, etc.

	More information about compiler toolchains, please [[Available Toolchains and Toolchain Compatibility]].		More information about compiler toolchains, please [[Available Toolchains and Toolchain Compatibility]].

Moses at 14:46, 6 September 2023

2023-09-06T14:46:58Z

Show changes

Shtsai at 02:30, 28 August 2020

2020-08-28T02:30:44Z

← Older revision		Revision as of 22:30, 27 August 2020
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	'''GNU compiler suites''':		'''GNU compiler suites''':

	*Version 4.4.7, provided by the GCC/4.4.7 module, includes C, C++, and Fortran compilers.
	*Version 4.8.5, this is the system default, available if no GCC modules are loaded.		*Version 4.8.5, this is the system default, available if no GCC modules are loaded.
	*Version 5.4.0, provided by the GCC/5.4.0-2.26 module, includes C, C++, and Fortran compilers.
	*Version 6.3.0, provided by the GCC/6.3.0-2.27 module, includes C, C++, and Fortran compilers.
	*Version 6.4.0, provided by the GCC/6.4.0-2.28 module, includes C, C++, and Fortran compilers.		*Version 6.4.0, provided by the GCC/6.4.0-2.28 module, includes C, C++, and Fortran compilers.
	*Version 7.2.0, provided by the GCC/7.2.0-2.29 module, includes C, C++, and Fortran compilers.		*Version 7.3.0, provided by the GCC/7.3.0-2.30 module, includes C, C++, and Fortran compilers.
			*Version 8.3.0, provided by the GCC/8.3.0 module, includes C, C++, and Fortran compilers.
			*Version 9.2.0, provided by the GCC/9.2.0 module, includes C, C++, and Fortran compilers.

	'''PGI compiler suites''':		'''PGI compiler suites''':

	*Version 17.9, provided by the PGI/17.9 module.		*Version 19.10, provided by the PGI/19.10-GCC-8.3.0-2.32 module.


Line 72:		Line 70:
	*Version 15.2, provided by the iccifort/2015.2.164-GCC-4.8.5 module.		*Version 15.2, provided by the iccifort/2015.2.164-GCC-4.8.5 module.
	*Version 18.0.1.163, provided by the iccifort/2018.1.163-GCC-6.4.0-2.28 module.		*Version 18.0.1.163, provided by the iccifort/2018.1.163-GCC-6.4.0-2.28 module.
			*Version 19.5.281, provided by the iccifort/2019.5.281 module.



	'''LLVM compiler suites'''':		'''LLVM compiler suites'''':

	*Version 3.8.1, provided by the LLVM/3.8.1-~~foss~~-~~2016b module~~.		*Version 8.0.1, provided by the LLVM/8.0.1-GCCcore-8.3.0 module.
	*Version 4.0.0~~, provided by the LLVM/4.0.0-foss-2016b~~ module.		*Version 9.0.0, provided by the LLVM/9.0.0-GCCcore-8.3.0 module.
	*Version 5.0.1, provided by the LLVM/5.0.1-GCCcore-6.4.0 module.		*Version 9.0.1, provided by the LLVM/9.0.1-GCCcore-8.3.0 module.
	*Version 6.0.0, provided by the LLVM/6.0.0-GCCcore-7.2.0 module.


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	</pre>		</pre>

	To use any of the compiler suite, please first load the corresponding module. For example, to use the GNU 6.4.0 compiler suite, load the module with		To use any of the compiler suite, please first load the corresponding module. For example, to use the GNU 8.3.0 compiler suite, load the module with
	<pre class="gcommand">		<pre class="gcommand">
	ml load GCC/6.4.0~~-2.28~~		ml load GCC/8.3.0
	</pre>		</pre>

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	The following foss toolchains are available:		The following foss toolchains are available:

	*foss/~~2016b~~, includes GCC 5.4.0, OpenMPI ~~1.10.~~3~~, OpenBLAS 0~~.~~2.18, FFTW 3.3.4, ScaLAPACK 2.0.2~~		*foss/2019b, includes GCC 8.3.0, OpenMPI 3.1.4, OpenBLAS 0.3.7, FFTW 3.3.8, ScaLAPACK 2.0.2
	*foss/2018a, includes GCC 6.4~~.0, OpenMPI 2.1.2~~, OpenBLAS 0.2.20, FFTW 3.3.7, ScaLAPACK 2.0.2

	When you load a toolchain, all it components will be loaded. For example:		When you load a toolchain, all it components will be loaded. For example:
	<pre class="gcommand">		<pre class="gcommand">
	ml foss/~~2016b~~		[shtsai@tcn12 ]$ ml foss/2019b
			[shtsai@tcn12 ]$ ml

			Currently Loaded Modules:
			1) GCCcore/8.3.0 9) hwloc/1.11.12-GCCcore-8.3.0
			2) zlib/1.2.11-GCCcore-8.3.0 10) OpenMPI/3.1.4-GCC-8.3.0
			3) binutils/2.32-GCCcore-8.3.0 11) OpenBLAS/0.3.7-GCC-8.3.0
			4) GCC/8.3.0 12) gompi/2019b
			5) numactl/2.0.12-GCCcore-8.3.0 13) FFTW/3.3.8-gompi-2019b
			6) XZ/5.2.4-GCCcore-8.3.0 14) ScaLAPACK/2.0.2-gompi-2019b
			7) libxml2/2.9.9-GCCcore-8.3.0 15) foss/2019b
			8) libpciaccess/0.14-GCCcore-8.3.0

	</pre>		</pre>
	~~will load these modules:~~
	*GCCcore/5.4.0
	*binutils/2.26-GCCcore-5.4.0
	*GCC/5.4.0-2.26
	*numactl/2.0.11-GCC-5.4.0-2.26
	*hwloc/1.11.3-GCC-5.4.0-2.26
	*OpenMPI/1.10.3-GCC-5.4.0-2.26
	*OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1
	*gompi/2016b
	*FFTW/3.3.4-gompi-2016b
	*ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1
	*foss/2016b



	----		----
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Shtsai at 14:48, 12 February 2019

2019-02-12T14:48:55Z

← Older revision		Revision as of 10:48, 12 February 2019
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	===Where should I compile my code?===		===Where should I compile my code?===

	You can compile the code ~~on the teaching cluster login node,~~ in an interactive session on a compute node, or on a compute node as a batch job.		You can compile the code in an interactive session on a compute node or on a compute node as a batch job.

	To compile the code in an interactive session, first start an interactive session using the command		To compile the code in an interactive session, first start an interactive session using the command
Line 10:		Line 10:
	</pre>		</pre>

			To compile the code in your batch job, please load the compiler module in your job submission script and include the code compilation line in your job submission script.

			Please note that it is '''not''' recommended to compile code on the teaching cluster login node, as it has a slightly newer processor type than the compute nodes and some compilers will automatically optimize the binaries for the processor where the code is compiled. When that happens, the binary might not run in the batch queue (it will experience an ''illegal instruction'' error).

	For information on how to access the compute node interactively for code compilation, please see [[Running Jobs on the teaching cluster]].		For information on how to access the compute node interactively for code compilation, please see [[Running Jobs on the teaching cluster]].

Shtsai: Created page with "Category:Teaching ===Where should I compile my code?=== You can compile the code on the teaching cluster login node, in an interactive session on a compute node, or on a..."

2019-01-06T02:48:10Z

Created page with "Category:Teaching ===Where should I compile my code?=== You can compile the code on the teaching cluster login node, in an interactive session on a compute node, or on a..."

New page

[[Category:Teaching]]

===Where should I compile my code?===

You can compile the code on the teaching cluster login node, in an interactive session on a compute node, or on a compute node as a batch job.

To compile the code in an interactive session, first start an interactive session using the command
<pre class="gcommand">
qlogin
</pre>

For information on how to access the compute node interactively for code compilation, please see [[Running Jobs on the teaching cluster]].

----

===Compilers===

A number of Fortran and C/C++ compilers are available on the teaching cluster, as well as Java and scripting languages such as Perl and Python.

'''Summary of main Fortran and C/C++ compilers installed:'''

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" |
! scope="col" | Portland Group (PGI)
! scope="col" | Intel
! scope="col" | GNU
! scope="col" | OpenMPI
! scope="col" | File extension
|-

| Fortran77 || pgf77 || ifort || || mpif77|| .f
|-
| Fortran90 || pgf90 || ifort || gfortran|| mpif90|| .f90
|-
| Fortran95 || pgf95 || ifort || gfortran || mpifort || .f95
|-
| C || pgcc || icc || gcc || mpicc || .c
|-
| C++ || pgCC || icpc || g++ || mpicxx || .C, .cpp, .cc
|-

|}

The various compiler suites are provided by their environment modules.

'''GNU compiler suites''':

*Version 4.4.7, provided by the GCC/4.4.7 module, includes C, C++, and Fortran compilers.
*Version 4.8.5, this is the system default, available if no GCC modules are loaded.
*Version 5.4.0, provided by the GCC/5.4.0-2.26 module, includes C, C++, and Fortran compilers.
*Version 6.3.0, provided by the GCC/6.3.0-2.27 module, includes C, C++, and Fortran compilers.
*Version 6.4.0, provided by the GCC/6.4.0-2.28 module, includes C, C++, and Fortran compilers.
*Version 7.2.0, provided by the GCC/7.2.0-2.29 module, includes C, C++, and Fortran compilers.

'''PGI compiler suites''':

*Version 17.9, provided by the PGI/17.9 module.

'''Intel compiler suites''':

*Version 13 SP1, provided by the iccifort/2013_sp1.0.080 module.
*Version 15.2, provided by the iccifort/2015.2.164-GCC-4.8.5 module.
*Version 18.0.1.163, provided by the iccifort/2018.1.163-GCC-6.4.0-2.28 module.

'''LLVM compiler suites'''':

*Version 3.8.1, provided by the LLVM/3.8.1-foss-2016b module.
*Version 4.0.0, provided by the LLVM/4.0.0-foss-2016b module.
*Version 5.0.1, provided by the LLVM/5.0.1-GCCcore-6.4.0 module.
*Version 6.0.0, provided by the LLVM/6.0.0-GCCcore-7.2.0 module.

The module spider command can be used to see information on the various modules available. For example, to check all GCC compiler suites installed, use
<pre class="gcommand">
ml spider gcc
</pre>

To use any of the compiler suite, please first load the corresponding module. For example, to use the GNU 6.4.0 compiler suite, load the module with
<pre class="gcommand">
ml load GCC/6.4.0-2.28
</pre>

Please note that you can only have one compiler module loaded at a time. For more information about Environment Modules, please see [[lmod-Sapelo2|lmod]].

====Some commonly used compiler options====

'''PGI compiler suite:'''

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Option
! scope="col" | Description
|-

| -O0 || Specifies no optimization, recommended for code debugging
|-
| -O1 || Specifies local optimization
|-
| -O2 || Specifies global optimization (this is the default, same as using -O)
|-
| -O3 || Includes -O1, -O2 and more aggressive optimization. Use with care.
|-
| -fast || Chooses generally good optimization options for the platform. Type pgcc -fast -help to see the equivalent options.
|-
| -Mbounds || Performs runtime array bound check, recommended for code debugging
|-
| -g || Produces symbolic debug information in the object files.
|-
| -r8 || Interpret REAL variables as DOUBLE PRECISION.
|-
| -B || Allow C++ style comments in C source code; these begin with ‘//’ and continue until the end of the current line. pgcc only.
|-
| -Kieee || Perform floating-point operations in strict conformance with the IEEE 754 standard. The default compilation is -Knoieee, which uses faster but very slightly less accurate methods.
|-
| -mp || Interpret OpenMP directives to explicitly parallelize regions of code for execution by multiple threads
|-
| -acc || Enable OpenACC pragmas and directives to explicitly parallelize regions of code for execution by accelerator devices. Use with the -ta option
|}

'''NOTE'''
When using optimization options, please check if your code becomes more efficient (in some cases optimization options will slow the code down) and if it still generates correct results. Many other compiler options are available. For more information on the PGI compilers, you can view the manual pages with the commands '''man pgf90''', '''man pgcc''', etc, after loading the pgi module.

'''Intel compiler suite:'''

{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
|-
! scope="col" | Option
! scope="col" | Description
|-

| -O0 || Specifies no optimization, recommended for code debugging
|-
| -O2 || Enables optimizations for speed. This is the generally recommended optimization level.
|-
| -O3 || Performs -O2 optimizations and more aggressive loop transformations. Use with care.
|-
| -fast || Chooses generally good optimization options for the platform. Type pgcc -fast -help to see the equivalent options.
|-
| -Mbounds || Performs runtime array bound check, recommended for code debugging
|}

----
[[#top|Back to Top]]

===Compiler Toolchains===

On the teaching cluster we use the [https://easybuild.readthedocs.io/en/latest/ EasyBuild] framework to install software applications. The EasyBuild toolchains are also available for users to compile their own code. Each toolchain provides a compiler suite and some basic libraries, such as MPI, BLAS, LAPACK, FFTW, etc.

'''foss toolchains:'''

Most software applications are installed with the '''foss''' toolchain, where '''foss''' is short for “Free and Open Source Software”.

The foss toolchain consists of:

*binutils (https://www.gnu.org/software/binutils/)
*the GNU Compiler Collection (GCC, https://gcc.gnu.org/), i.e. gcc (C), g++ (C++) and gfortran (Fortran)
*the Open MPI library (https://www.open-mpi.org/)
*the OpenBLAS (http://www.openblas.net/) + LAPACK (http://netlib.org/lapack) libraries
*the ScaLAPACK (http://netlib.org/scalapack) library is also included
*the FFTW library (http://fftw.org/)

The following foss toolchains are available:

*foss/2016b, includes GCC 5.4.0, OpenMPI 1.10.3, OpenBLAS 0.2.18, FFTW 3.3.4, ScaLAPACK 2.0.2
*foss/2018a, includes GCC 6.4.0, OpenMPI 2.1.2, OpenBLAS 0.2.20, FFTW 3.3.7, ScaLAPACK 2.0.2

When you load a toolchain, all it components will be loaded. For example:
<pre class="gcommand">
ml foss/2016b
</pre>
will load these modules:
*GCCcore/5.4.0
*binutils/2.26-GCCcore-5.4.0
*GCC/5.4.0-2.26
*numactl/2.0.11-GCC-5.4.0-2.26
*hwloc/1.11.3-GCC-5.4.0-2.26
*OpenMPI/1.10.3-GCC-5.4.0-2.26
*OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1
*gompi/2016b
*FFTW/3.3.4-gompi-2016b
*ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1
*foss/2016b

----
[[#top|Back to Top]]