Compiling Code on Quest

A introduction to compilations strategies on QUEST

Basic Compiling Strategies

Quest users have the choice of GNU's gcc/gfortran and Intel's icc/ifort compilers to compile their codes. In addition to being accessible as modules, the GNU compilers are also provided by the operating system (RedHat Enterprise Linux). These compilers are sometimes referred to as native in the Quest documentation. More up-to-date versions are provided as modules (see Modules on Quest). When attempting to compile code on Quest, it is critical to follow these general steps

1. Identify an appropriate compiler
2. Identify external dependencies
3. Identify which libraries contain the external function calls we make from our program
4. Identify where these external dependencies live on the system

Compilers

• GCC (The GNU Compiler Collection providing gcc and gfortran for compiling C and Fortran programs
• Intel ® Cluster Toolkit (consisting of icc/ifort for compiling C and Fortran programs, as well as Intel MPI Library for compiling MPI parallelized codes)
• MPI (Message Passing Interface) compilers such as OpenMPI and MPICH

See available versions of the compilers with

module spider gcc

module spider intel



module spider mpi

Libraries/Dependencies

After identifying the compiler that suites your needs, you must identify what dependencies your program has, and where they can be found on Quest. External dependencies can generally be found either on the system (note recommended), by loading modules, or by installing these dependencies yourself using a service like anaconda to create virtual environments. A common pitfall when compiling code on a HPC cluster like Quest, is accidentally linking against system libraries that may exist on the log-in machines, but do not exist on the compute nodes where you program actually runs.

Examples

The example we will be using can be found here. On Quest, you can run

wget https://raw.githubusercontent.com/CIERA-Northwestern/cmake_tutorial/enhanced_tutorial/Makefile/example.c

to get the example C code used for this documentation onto Quest. This C program has the following dependencies.

• An MPI compiler
• HDF5 and HDF5_HL C Libraries
• GSL C Libraries

Configuring a Makefile

To make a Makefile, we will first construct a compilation command by hand. To do this, we will follow the four steps outlined above, the answers to questions 1-3 can be captured fairly easily. For the answer to question 4, we explore the multiple possibilities in more details.

1. Identify an appropriate compiler: mpicc which is found by running module load mpi/openmpi-4.0.5-intel-19.0.5.281
2. Identify external dependencies: GSL and HDF5 C Libraries and Headers
3. Identify which libraries contain the external function calls we make from our program: -lgsl -lgslcblas -lm -lhdf5 -lhdf5_hl
4. Identify where these external dependencies live on the system

In general, there are three viable options for the answer to question 4 and we discuss them below.

System Level:Although there are some packages installed at the system level on both the log-in nodes and the compute nodes, relying on these is the least desirable outcome. This is for two reasons, 1.) it is hard to know ahead of time which libraries exists on both log-in and compute nodes and not just the log-in nodes and b.) they tend to be quite old and not optimized versions of a given package. When we refer to system level libraries, we refer to those packages which live in standard locations such as

/usr/lib:/usr/lib64/:/usr/local/lib

and are installed via the package manager yum.

Modules:Modules provide the optimal way to locate external dependencies on Quest. This is true for two reasons. First, they are installed in a shared location such that all users on all log-in and compute nodes can access and use them. That is, if you compile a program against modules, and send your program to a fellow colleague who also uses Quest, they can run your program since they can load and use the same libraries that you used. Second, these libraries tend to be more recent versions of the relevant dependency and are optimally compiled for running on Quest.

Virtual/Anaconda Environments: Anaconda is a software management tool which allows users to create isolated folders, called environments that contain working (and generally more recent) versions of Python, C/C++/Fortran and R libraries. Moreover, these environments can be installed in locations on the filesystem in which the user has permissions to read/write/execute files.

We now will demonstrate compiling our example code by hand/with a Makefile with respect to these three options for identifying where your program's external dependencies live on the system.

System Level

How do you know when you have linked against a library installed on the system and what do that look like? After loading the MPI module that contains our compiler we need, we can go ahead and run the compile command without specifying any specific location for where the libraries live

mpicc example.c -lgsl -lgslcblas -lm -lhdf5 -lhdf5_hl -o example

This command will compile, and the reason for this is because HDF5 and GSL happen to be installed at the system level on the log-in nodes. We can verify the libraries that your program is linked against by running the command ldd.

[quser22 Makefile]$ ldd example
	libgsl.so.0 => /usr/lib64/libgsl.so.0 (0x00002b6117685000)
	libgslcblas.so.0 => /usr/lib64/libgslcblas.so.0 (0x00002b6117aae000)
	libm.so.6 => /usr/lib64/libm.so.6 (0x00002b6117ceb000)
	libhdf5.so.8 => /usr/lib64/libhdf5.so.8 (0x00002b6117fed000)
	libhdf5_hl.so.8 => /usr/lib64/libhdf5_hl.so.8 (0x00002b6118493000)

Modules

Let us compile this same code, using modules. First, we search for viable modules for these two dependencies. Second. when deciding which one to use, it is important to try to load a module that was compiled using the same compiler and version as the one you choose to compiler your program. In our case intel-19.0.5.281

$ module spider hdf5

$ module spider gsl

Looking at the options, we see two modules that fit the bill:

module load hdf5/1.10.7-openmpi-4.0.5-intel-19.0.5.281
module load gsl/2.5-intel-19.0.5.281

Let's use the same compile command to compile the code now.

mpicc example.c -lgsl -lgslcblas -lm -lhdf5 -lhdf5_hl -o example

That is it, right? Well, if we check to see which libraries example is linked against, we see that they have not changed:

[quser22 Makefile]$ ldd example
	libgsl.so.0 => /usr/lib64/libgsl.so.0 (0x00002b6117685000)
	libgslcblas.so.0 => /usr/lib64/libgslcblas.so.0 (0x00002b6117aae000)
	libm.so.6 => /usr/lib64/libm.so.6 (0x00002b6117ceb000)
	libhdf5.so.8 => /usr/lib64/libhdf5.so.8 (0x00002b6117fed000)
	libhdf5_hl.so.8 => /usr/lib64/libhdf5_hl.so.8 (0x00002b6118493000)

The reason for this is because the libraries live in non-standard paths on the system. Therefore, we must explicitly tell the compiler where the directories which have the header files (-I) and which have the libraries (-L) are on the system. Let us try this with the HDF5 libraries and see the difference. To find the PATHS to the libraries and header files, we can run

module show hdf5/1.10.7-openmpi-4.0.5-intel-19.0.5.281

Having done this, we can now try running the command as follows.

[quser24 Makefile]$ mpicc -I/hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/hdf5-1.10.7-slwfvnxqgb353tf4ltetdeka6ryccz7y/include example.c -L/hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/hdf5-1.10.7-slwfvnxqgb353tf4ltetdeka6ryccz7y/lib/ -lgsl -lgslcblas -lm -lhdf5 -lhdf5_hl -o example

Now when we check which hdf5 libraries example linked against, they are, in fact, the libraries provided by the modules.

[quser22 Makefile]$ ldd example
	....
	....
	libhdf5.so.103 => /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/hdf5-1.10.7-slwfvnxqgb353tf4ltetdeka6ryccz7y/lib/libhdf5.so.103 (0x00002ac8fcee1000)
	libhdf5_hl.so.100 => /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/hdf5-1.10.7-slwfvnxqgb353tf4ltetdeka6ryccz7y/lib/libhdf5_hl.so.100 (0x00002ac8fd72c000)

Similarly, we can add the -I and -L for the location of the gsl libraries. You may be thinking that if you had a lot of external dependencies for your code, that constructing the correct command line by hand would be difficult and time consuming, and you would be right. That is why most packages are built using tools like autoconf or CMake.

Anaconda

To see if anaconda contains the software you need, and to see what the package is called on anaconda, you can search anaconda cloud. An example of searching anaconda cloud for the HDF5 library can be found here. To start, we load the anaconda module and create a virtual environment.

module purge all
module load python/anaconda3.6
conda create --name makefile-test gsl hdf5 openmpi-mpicc --yes
source activate makefile-test

Let's use the same compile command to compile the code now.

mpicc example.c -lgsl -lgslcblas -lm -lhdf5 -lhdf5_hl -o example

Unlike with modules, no further work is needed to specify special non-standard directories for where the libraries live. This is because you have installed a compiler directly into the virtual environment, and, therefore, the compiler considers all directories inside of the environmnet to be "standard locations".

(makefile-test) [quser22 Makefile]$ ldd example
	libgsl.so.23 => /home/netid/.conda/envs/makefile-test/lib/libgsl.so.23 (0x00002ba14e1f7000)
	libgslcblas.so.0 => /home/netid/.conda/envs/makefile-test/lib/libgslcblas.so.0 (0x00002ba14e67a000)
	libhdf5.so.103 => /home/netid/.conda/envs/makefile-test/lib/libhdf5.so.103 (0x00002ba14ebc3000)
	libhdf5_hl.so.100 => /home/netid/.conda/envs/makefile-test/lib/libhdf5_hl.so.100 (0x00002ba14e025000)

 

Autoconf

Autoconf is a tool which produces shell scripts that automatically configure your package. To start, we create a configure.ac which holds the answers to questions 1-3 of our guidelines to compiling code

• Identify an appropriate compiler
• Identify external dependencies
• Identify which libraries contain the external function calls we make from our program

configure.ac

AC_INIT(example, 1.0)

# Step 1: Appropriate (working) compiler
AC_PROG_CC([mpicc])

# Step 2a: Ensure that you can find the external headers
AC_CHECK_HEADERS(hdf5.h)
AC_CHECK_HEADERS(gsl/gsl_sf_bessel.h)

# Step 3: Make sure that the external libraries contain the function calls that you make
# and check where those libraries live on the system
AC_CHECK_LIB(hdf5, H5open)
AC_CHECK_LIB(hdf5_hl, H5TBread_table)
AC_CHECK_LIB(gsl, gsl_sf_bessel_J0)

# Process Makefile.in to create Makefile
AC_OUTPUT(Makefile)

In order to propagate the information that is found by configure.ac, we need to create a template Makefile called Makefile.in that contains the variables which will be auto-populated during the ./configure stage of the build process.

Makefile.in

CC=@CC@
LD=@CC@
CFLAGS=@CFLAGS@
LDFLAGS=@LDFLAGS@
LIBS=@LIBS@

example: example.o
    $(LD) -o $@ $^ $(LDFLAGS) $(LIBS)

With only loading the MPI module, we can see how autoconf populates these variables.

[quser22 AutoConf]$ autoconf && ./configure
...
...
[quser22 AutoConf]$ cat Makefile
CC=mpicc
LD=mpicc
CFLAGS=-g -O2
LDFLAGS=
LIBS=-lgsl -lhdf5_hl -lhdf5 

example: example.o
	$(LD) -o $@ $^ $(LDFLAGS) $(LIBS)

.PHONY: clean
clean:
	rm -f example *.o

You can see that most of the information is populated automatically, including what libraries contain the external function calls that our program makes. However, similar to our hand-constructed Makefile, we can send in alternative locations for where our libraries live on the system by defining the LDFLAGS variable before we called ./configure.

[quser22 AutoConf]$ autoconf && LDFLAGS=$(echo $LD_LIBRARY_PATH | echo "-L" $(sed 's/:/ -L /g')) ./configure
...
...
[quser22 AutoConf]$ cat Makefile
CC=mpicc
LD=mpicc
CFLAGS=-g -O2
LDFLAGS=-L /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/gsl-2.5-ioov7cjw6tqqvtzuukzfkt3evh5odjkl/lib -L /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/hdf5-1.10.7-slwfvnxqgb353tf4ltetdeka6ryccz7y/lib -L /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/libszip-2.1.1-vzorkozqk5vkfxzcybqasxzapt3iw2a5/lib -L /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/openmpi-4.0.5-phpnhxevtv3uq37z7rugq4rwfbxbdcgg/lib -L /hpc/software/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/zlib-1.2.11-ytzoecnlatvnfsvkaist7ddqu3wc2mo3/lib -L /usr/local/ucx-1.8.1/lib64 -L /usr/local/ucx-1.8.1/lib -L /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/numactl-2.0.12-guzt226gnmybpkje5iqja3efcprwsrjx/lib -L /usr/local/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/hwloc-2.1.0-xvch25aylytjrzei5gf26fwrugybnhlr/lib -L /software/intel/2019.5/debugger_2019/libipt/intel64/lib -L /software/intel/2019.5/compilers_and_libraries_2019.5.281/linux/daal/../tbb/lib/intel64_lin/gcc4.4 -L /software/intel/2019.5/compilers_and_libraries_2019.5.281/linux/daal/lib/intel64_lin -L /software/intel/2019.5/compilers_and_libraries_2019.5.281/linux/tbb/lib/intel64/gcc4.7 -L /software/intel/2019.5/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin -L /software/intel/2019.5/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin -L /software/intel/2019.5/compilers_and_libraries_2019.5.281/linux/ipp/lib/intel64_lin
LIBS=-lgsl -lhdf5_hl -lhdf5 

example: example.o
	$(LD) -o $@ $^ $(LDFLAGS) $(LIBS)

.PHONY: clean
clean:
	rm -f example *.o

Now, just as with the Makefile we made by hand, we simply run make and ensure that the program is linked to the right libraries using the ldd command.

[quser22 AutoConf]$ make
[quser22 AutoConf]$ ldd example
	libgsl.so.23 => /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/gsl-2.5-ioov7cjw6tqqvtzuukzfkt3evh5odjkl/lib/libgsl.so.23 (0x00002b85863b0000)
	libhdf5_hl.so.100 => /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/hdf5-1.10.7-slwfvnxqgb353tf4ltetdeka6ryccz7y/lib/libhdf5_hl.so.100 (0x00002b8586dad000)
	libhdf5.so.103 => /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/hdf5-1.10.7-slwfvnxqgb353tf4ltetdeka6ryccz7y/lib/libhdf5.so.103 (0x00002b8586fda000)

CMake

CMake is similar to autoconf, but has a more abstract and arguably more intuitive structure to its configuration files. As with all of these compilation options, we do the following:

• Identify an appropriate compiler
• Identify external dependencies
• Identify which libraries contain the external function calls we make from our program

CMakeLists.txt

# CMakeTutorial
cmake_minimum_required(VERSION 3.10 FATAL_ERROR)

# step 1 what language is this code in (this determines what compiler is looked for by CMake)
project(CMakeTutorial VERSION 1.0.0 LANGUAGES C)

# Step 2: Identify external packages and whether they are required to be discoverable and usable for compilation.
find_package(MPI REQUIRED)
find_package(GSL REQUIRED)
find_package(HDF5 COMPONENTS C HL REQUIRED)

# Where is the source code
add_subdirectory(src)

This is the top level configuration files for CMake and it does a lot of the heavy lifting. We then point at subsequent CMakeLists.txt configuration files (i.e. the configuration file in add_subdirectory(src)) which then explicitly links the automatically discovered libraries to our program. With CMake, it is enough to load the modules containing our dependencies, as CMake will automatically search LD_LIBRARY_PATH in order to discover the module libraries before it discoveries the libraries installed on the system.

./src/CMakeLists.txt

# CMakeTutorial
# add the executable
add_executable(example example.c)

# add the automatically found path to the external header files needed
include_directories(SYSTEM ${HDF5_INCLUDE_DIRS})
include_directories(SYSTEM ${MPI_INCLUDE_DIRS})
include_directories(SYSTEM ${GSL_INCLUDE_DIRS})

# link against the automatically discovered libraries (which includes the library and path to where it is on the system)
target_link_libraries(example ${HDF5_LIBRARIES})
target_link_libraries(example ${HDF5_HL_LIBRARIES})
target_link_libraries(example ${GSL_LIBRARIES})
target_link_libraries(example ${MPI_LIBRARIES} ${MPI_LINK_FLAGS})

# When you run make install where would you like the executable to go
install(TARGETS example DESTINATION bin)

To compile, we invoke the cmake command and point to the top-level directory. It is common practice to not run the cmake configuartion and build steps in the same directory as the top-level CMake configuration file, and instead, to make a new directory and run the commands from there.

module purge all
module load cmake/3.15.4 
module load mpi/openmpi-4.0.5-intel-19.0.5.281 
module load hdf5/1.10.7-openmpi-4.0.5-intel-19.0.5.281 
module load gsl/2.5-intel-19.0.5.281

# make a directory to run the configuration and build steps in
mkdir build
cd build
# You can overide the C compiler to be used by CMake by modifying the environmnetal variable CC. Also, you can tell CMake where you would like to install the code (the default location is somewhere where Quest users do not have permissions to install) by passing a relative or absolutel path to the argument -DCMAKE_INSTALL_PREFIX
CC=mpicc cmake .. -DCMAKE_INSTALL_PREFIX=.
make install

-- The C compiler identification is Intel 19.0.5.20190815
-- Check for working C compiler: /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/openmpi-4.0.5-phpnhxevtv3uq37z7rugq4rwfbxbdcgg/bin/mpicc
-- Check for working C compiler: /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/openmpi-4.0.5-phpnhxevtv3uq37z7rugq4rwfbxbdcgg/bin/mpicc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found MPI_C: /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/openmpi-4.0.5-phpnhxevtv3uq37z7rugq4rwfbxbdcgg/bin/mpicc (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") 
-- Found GSL: /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/gsl-2.5-ioov7cjw6tqqvtzuukzfkt3evh5odjkl/include (found version "2.5") 
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/hdf5-1.10.7-slwfvnxqgb353tf4ltetdeka6ryccz7y/lib/libhdf5.so;/hpc/software/spack/opt/spack/linux-rhel7-x86_64/intel-19.0.5.281/libszip-2.1.1-vzorkozqk5vkfxzcybqasxzapt3iw2a5/lib/libsz.so;/hpc/software/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/zlib-1.2.11-ytzoecnlatvnfsvkaist7ddqu3wc2mo3/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.7") found components:  C HL 
-- Configuring done
-- Generating done
-- Build files have been written to: /projects/a9009/sbc538/documentation/108820/cmake_tutorial/cmake/build

Here you can see that in the configuration stage of CMake, you will already be told which libraries (system, module or otherwise) that CMake will link your program to, and so using the ldd command is unnecessary.

 

Singularity

Last, but not least, building your software inside of a container can be an impactful and long term solution for building and distributing your software. The benefit of containers is that at the time of building the container, you have sudo privileges, and so, within the container you can install all of your dependencies into the system library locations. Also, once constructed, your container is entirely portable as is, because the versions of the dependecies that you install inside of the container will live inside the container forever, untouched. Below, we start with a container that has Ubuntu 20.10 already installed (i.e. we bootstrap our container from this container), and use apt-get to install only the bare minimum extra packages that we need to compile our code.

example.def

Bootstrap: docker
From: ubuntu:groovy-20210225

%post
    # Upgrade system libraries for ubuntu 20.10 and install libraries we need for our program
    apt-get -y update && apt-get -y install libopenmpi-dev openmpi-bin libhdf5-serial-dev libgsl-dev libgslcblas0 cmake git
    # Clone source code
    git clone https://github.com/CIERA-Northwestern/cmake_tutorial.git /cmake_tutorial
    cd /cmake_tutorial
    # checkout branch of code
    git checkout enhanced_tutorial
    # run cmake commands
    cd cmake
    mkdir -p build
    cd build
    CC=mpicc cmake .. -DCMAKE_INSTALL_PREFIX=/opt/local/
    make install
%runscript
    /opt/local/bin/example

To build this recipe, we run

module load singularity
singularity build --remote example.simg example.def

For more information on containers, please see using singularity on Quest.