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Spack Introduction and Environment Setup

What is Spack?

Spack is a package manager, similar to yum, apt-get, or conda. I It allows for multiple package versions/configurations.  Unlike  Unlike the other package managers listed, Spack is specifically designed to be used on HPC resources with varying architectures. 

The purpose of this documentation is to provide a practical guide to quickly enable you to take advantage of its use in your research.

How to set up your environment to use Spack

First, log in to one of the gateway nodes; here, we are logging onto pascal:

...

Next, add the following code to your ~/.bashrc, which will automatically load Spack into your shell on all servers besides gateways:

# detect kernel version, then source spack file if it exists
_KERNEL_VERSION=$(uname -r | cut -d '.' -f1,2,3)
 
if [[ "${HOSTNAME}" != "pascal.med.cornell.edu" ]] || [[ "${HOSTNAME}" != "aphrodite.med.cornell.edu" ]] || [[ "${HOSTNAME}" != "aristotle.med.cornell.edu" ]]; then
         if if [[ "${_KERNEL_VERSION}" == *"2.6.3"* ]] ; then
            if 
        if [ -f /softlib/apps/EL6/spack/share/spack/setup-env.sh ] ; then
                    
            . /softlib/apps/EL6/spack/share/spack/setup-env.sh
                    fifi
    fi    
    if [[ "${KERNEL fi
    if [[ "${_KERNEL_VERSION}" ==  *"3.10"* ]] ; then
            if 
        if [ -f /softlibsoftware/appsspack/EL7/spackcentos7/share/spack/setup-env.sh ] ; then
                    
            . /softlibsoftware/appsspack/EL7/spackcentos7/share/spack/setup-env.sh
            fi
    fi
 
fi

Package Information

How to show what packages are installed in Spack

The Spack Basic Usage guide demonstrates how to show which packages are already present in Spack though we will show them here as well.

To see all packages currently installed, use this command:

spack find

==> 1027 installed packages.
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
autoconf@2.69    fftw@3.3.7         libjpeg-turbo@1.5.90  openmpi@3.0.1           py-six@1.10.0
autoconf@2
        elif [ -f /software/spack/share/spack/setup-env.sh ] ; then
            . /software/spack/share/spack/setup-env.sh
        fi
    fi
fi
builtin unset _KERNEL_VERSION

...

Package Information

How to show what packages are installed in Spack

The Spack Basic Usage guide demonstrates how to show which packages are already present in Spack though we will show them here as well.

To see all packages currently installed, use this command:

spack find

==> 1027 installed packages.
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
autoconf@2.69    fftw@3.3.7         

...

libjpeg-turbo@1.

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5.

...

90  

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openmpi@3.0.1           

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py-six@1.

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10.

...

0
autoconf@2.69    fftw@3.3.7         libpciaccess@0.13.

...

4   openmpi@3.0.1           python@2.7.

...

13
autoconf@2.69    fftw@3.3.

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7         

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libpciaccess@0.

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13.5   

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openmpi@3.0.1           

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python@2.

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7.

...

14

...

autoconf@2.

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69    fftw@3.3.8         libpng@1.6.

...

27         openmpi@3.0.1           python@3.

...

4.

...

3
automake@1.15    fftw@3.3.8         libpng@1.6.29         openmpi@3.0.1           python@3.5.2
automake@1.16.1  fftw@3.3.8         libpthread-stubs@0.4  openmpi@3.0.1           python@3.5.2
automake@1.16.1  flex@2.6.3         libsigsegv@2.11       openmpi@3.0.1           python@3.6.0
binutils@2.28    fltk@1.3.3         libtiff@4.0.9         openmpi@3.1.0           readline@7.0
binutils@2.28    fltk@1.3.3         libtool@2.4.6         openssl@1               readline@7.0
bison@3.0.4      font-util@1.3.1    libx11@1.6.5          openssl@1               readline@7.0
boost@1.64.0     fontconfig@2.11.1  libxau@1.0.8          openssl@1.0.2k          relion@2.0.3
bowtie2@2.3.1    fontconfig@2.12.1  libxcb@1.13           openssl@1.0.2k          relion@2.0.3
bwa@0.7.15       freetype@2.7       libxdmcp@1.1.2        openssl@1.0.2n          relion@2.1
bzip2@1.0.6      freetype@2.7.1     libxml2@2.9.4         pcre@8.40               relion@2.1
cairo@1.14.8     gcc@6.3.0          libxml2@2.9.4         perl@5.24.1             relion@2.1
cairo@1.14.8     gdbm@1.13          libxml2@2.9.8         perl@5.26.2             relion@2.1
cmake@3.7.2      gdbm@1.14.1        libxslt@1.1.28        perl-text-soundex@3.05  relion@2.1
cmake@3.8.0      gettext@0.19.8.1   libxslt@1.1.29        pixman@0.34.0           relion@2.1
cmake@3.9.4      glib@2.49.7        libxslt@1.1.29        pixman@0.34.0           relion@2.1
cmake@3.9.4      glib@2.53.1        lz4@1.8.1.2           pkg-config@0.29.2       relion@3.0_beta
cmake@3.9.4      gmp@6.1.2          lzma@4.32.7           pkgconf@1.3.10          relion@3.0_beta
cmake@3.10.0     help2man@1.47.4    lzo@2.09              pkgconf@1.4.2           relion@3.0_beta
cmake@3.11.2     hmmer@3.1b2        m4@1.4.18             py-appdirs@1.4.3        relion@3.0_beta

Currently, there are 1027 packages (including different versions of the same package) installed. This number will undoubtably increase after the writing of this documentation.

Note: the name of each package is given, as well as the version number (e.g.autoconf@2.69). Also notice that the packages are also grouped by the OS and compiler that was used to construct the packages (e.g.linux-rhel6-x86_64 / gcc@4.4.6).

How to search the output of: spack find

However, while spack find list the packages alphabetically, it can still be a little difficult to search for packages you are interested in (especially if you don't know its exact/full name). For example, this command doesn't find any packages:

spack find py

However, from the output of the command spack find clearly shows numerous packages that start with "py". To improve on Spack's native find command, add this to your ~/.bashrc:

function spack_my_find () {
    spack find | sed -r "s/\x1B\[([0-9]{1,2}(;[0-9]{1,2})?)?[m|K]//g" | grep -E "${1}|-- linux" | sed 's/-- linux/\n-- linux/g'
}

This code provides the command spack_my_find, which provides a much more robust search of what's installed in Spack; specifically, it allows you to search for any package that contains a given string (regular expressions are supported). For example,

...

-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
relion@3.0_beta
relion@3.0_beta
relion@3.0_beta
relion@3.0_beta

-- linux-centos7-x86_64 / gcc@6.3.0 -----------------------------

Getting information about installed packages

...

spack find -v -l relion@3.0_beta

In the above command:

• The -v will cause the variants (e.g. compile-time options in package configuration) to be printed. This will allow us to see differences between the 2 packages.

• The -l will cause the package "hashes" to be printed.

Note: a hash is a fixed-length string that is calculated by a hash function, with the software/package of interest as the primary input. If 2 pieces of code have ANY differences, then they will have different hashes. Spack simply uses hashes to, among other things, provide a unique descriptor for each package.

...

Second, notice that each packages variants are printed with either a + or ~, indicating that an option is either included or not. For example, the first package (/u6dzm4v) does not include CUDA (~cuda), whereas the second package (/olcttts) does include CUDA (+cuda). Next, I'll describe how I learn more information about what the various package variants mean for a given package.

...

In the previous section, we observed that packages can have different variants (e.g. compile-time options). However, spack find -l -v prints abbreviated variant names, which can sometimes be cryptic. For a more complete description of a packages potential variants (as  well as versions/dependencies), use this command (here, we're looking at Relion, but you could enter any package name):

...

TRUNCATED OUTPUT:

==> 28316768 packages.
abinit                           muster                                 r-catools
abyss                            mvapich2                               r-cdcfluview
accfft                           mxml                                   r-cellranger
ack                              mxnet                                  r-cghflasso
activeharmony                    nag                                    r-checkmate
adept-utils                      nalu                                   r-checkpoint
adios                            nalu-wind                              r-chemometrics
adios2                           namd                                   r-chron
adlbx                            nano                                   r-circlize
adol-c                           nanoflann                              r-class
aegean                           nanopb                                 r-classint
albany                           nasm                                   r-cli

Currently, there are 2are 6,831 768 packages available! This number will also certainly increase after the writing of this documentation. 

Note: That the output of spack list is plain text, so searching its output is easier than searching the output of spack find

To search this output, just grep its output:

...

==> 19 installed packages.
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
python@2.7.13  python@2.7.14  python@3.4.3  python@3.5.2  python@3.5.2  python@3.6.0

-- linux-centos7-x86_64 / gcc@6.3.0 ------------------------------
python@2.7.13  python@2.7.14  python@2.7.14  python@2.7.15  python@3.4.3  python@3.6.0  python@3.7.0
python@2.7.13  python@2.7.14  python@2.7.15  python@2.7.15  python@3.5.2  python@3.6.2

Notice that there are multiple installations of python, that differ in version number, compiler, etc. As such, it is always a good idea to use the command spack find to observe if there are multiple installations before just loading a package blindly (otherwise you may load an installation that you do not intend).

To load the installation of python v. 3.7.0 that was compiled with GCC v. 6.3.0, use this command:

spack load -r python@3.7.0^gcc@6.3.0

• The -r instructs Spack to load all modules that python@3.7.0 depends on. This is typically done automatically, but not currently done for perl, python, or R (this is because Spack does not build these packages with RPATH support--this may change in the future).

...

python@2.7.13  python@2.7.14  python@2.7.14  python@2.7.15  python@3.4.3  python@3.6.0  python@3.7.0
python@2.7.13  python@2.7.14  python@2.7.15  python@2.7.15  python@3.5.2  python@3.6.2

Notice that there are multiple installations of python, that differ in version number, compiler, etc. As such, it is always a good idea to use the command spack find to observe if there are multiple installations before just loading a package blindly (otherwise you may load an installation that you do not intend).

To load the installation of python v. 3.7.0 that was compiled with GCC v. 6.3.0, use this command:

spack load -r python@3.7.0^gcc@6.3.0

• The -r instructs Spack to load all modules that python@3.7.0depends on. This is typically done automatically, but not currently done for perl, python, or R (this is because Spack does not build these packages with RPATH support--this may change in the future).

Executing this command doesn't produce any output, but just to illustrate that python@3.7.0 is indeed loaded (as well as its dependencies), execute the following command:

echo $LOADEDMODULES | sed "s/:/\n/g" | sort

Here, we can see that python@3.7.0is indeed loaded, as are all packages that it depends on.

How to use a unload package

To avoid confusion, as well as conserve memory, you may wish to unload a Spack package (this is especially true in complex workflows). Doing so is very easy:

spack unload python@3.7.0

Let's check and make sure we have really unloaded python@3.7.0:

echo $LOADEDMODULES | sed "s/:/\n/g" | sort

Here, we can see that python@3.7.0 is indeed loaded, as are all packages that it depends on.

...

OUTPUT:

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