Running on Edison

ULFM configuration for NERSC Edison

Edison is a Cray XC30, with a peak performance of 2.57 petaflops/sec, 133,824 compute cores, 357 terabytes of memory, and 7.56 petabytes of disk. Hosted at NERSC, it offers access to many researchers and practitioners in the US.

Installing the latest versions of Open MPI (including the development, unstable and stable) on this machine can easily be done by using the provided platform file. The same cannot unfortunately be said about the current ULFM version. This version was based on an older unstable version of Open MPI (1.7) and didnt backported all the new exciting features from the development branch of Open MPI. As a result, getting it to work on Edison is a little challenging, but we all like a little challenge.

Preparing for installation

This step is unfortunately required, as I couldnt find any other way to update the m4 file of our ancient ULFM installation, without dedicating too much time to such a hopeless task (especially as the new ULFM 2.0 is reaching almost stable status). The issue is triggered by a misconfiguration of autoconf 2.69 on Edison, which breaks all the autotool chain. The issue can be easily corrected by downloading the Mercurial version of ULFM on another computer, running autogen.sh, a quick configure with no arguments, followed by “make dist”. This will generate 2 archives (openmpi-1.7.1ULFM.tar.bz2 and openmpi-1.7.1ULFM.tar.gz). Use the one corresponding to your preferred compression algorithm, and move it on Edison.

Compiling from source

With the archive moved on Edison, you can now undergo the last step to configure and compile ULFM there. Lets assume we want to build an optimized version, integrated with Edison resource management software (Slurm), using uGNI, without debugging information. One of the interesting features ULFM inherited from Open MPI is the capability of using platform files. Here is the platform file for Edison, it will eventually make its way into the official ULFM release, meanwhile you can copy and paste directly from here.

enable_visibility=no
enable_static=no
enable_shared=yes
with_threads=no
enable_pretty_print_stacktrace=no
enable_dlopen=no
with_portals_config=redstorm
enable_mca_no_build=coll-hierarch,pml-dr,pml-v
enable_contrib_no_build=libnbc,vt
with_rte_support=yes
enable_heterogeneous=no
enable_pty_support=no
enable_mem_debug=no
enable_mem_profile=no
enable_binaries=yes
enable_script_wrapper_compilers=yes
ompi_cv_c_word_size_align=no
enable_mpi_ext=ftmpi
with_ft=mpi
with_openib=no
with_devel_headers=yes
with_alps=no
with_slurm=yes
with_xpmem=/opt/cray/xpmem/default
with_pmi=/opt/cray/pmi/default
with_cray_pmi2_ext=yes
with_ugni=/opt/cray/ugni/default
with_ugni_includedir=/opt/cray/gni-headers/default/include
with_io_romio_flags=--with-file-system=ufs+nfs
with_memory_manager=ptmalloc2
with_valgrind=no

With this platform file saved as platform.edisonyou can now proceed to configure ULFM using “./configure —with-platform=platform.edison …”. There are many other possible configuration parameters, and you are strongly encouraged to read the output of configure —helpto gain more insight into the flexible configuration system. Meanwhile here is what I usually add in addition to the platform file “—prefix=… –enable-mpirun-prefix-by-default” (please replace the dots with your prefered installation directory). Keep in mind that the installation directory must be in your $PATH, to have direct access to the wrapper compilers and to the mpiexec.

Preparing for execution

In general we suggest you to use a specific MCA file (the -am parameter) to provide the parameters for your ULFM runs (and not collide with the normal Open MPI runs). As long as you use mpiexec to start your application this will work. If instead you want to rely on srun to so do, you will have to dump the context of your AMCA file directly into your main ${HOME}/.openmpi/mca-params.conf file (and pay attention when you execute normal Open MPI runs).

Running ULFM applications in an interactive job

Congratulations, the hardest steps are now done and you are now supposed to have a fully compiled and ready to run version of ULFM, and its binaries in your $PATH. Allocating an interactive job on Edison is well described in the online documentation. There is however a trick, you need to add an option to prevent Slurm from destroying your job when one of the processes disappear. This option is —no-kill.

Thus, allocating an interactive job with 4 processes for a short duration can be achieved with “`salloc -p debug -N 4 –no-kill“.
Running an application then become easy, as indicated in ULFM setup steps.

Survival readiness

You code has now a sane execution environment that is able to survive faults, and can help your application achieve the same goal.

Uniform Intercomm Creation

A question about uniformly creating an inter-communicator using MPI_Intercomm_create has been posted on the ULFM mailing list. Initially, I though it is an easy corner-case, that can be solved with few barriers and/or agreements. It turns out this issue is more complicated that initially expected, with few twists on the way. Let me detail our adventure toward writing a uniform intercomm creation function.

Before moving further, let’s clarify what MPI_Intercomm_create is about. The MPI standard is not very explicit about the scope of this function, but we can gather enough info to start talking about (page 262 line 6):

This call [MPI_Intercomm_create] creates an inter-communicator. It is collective over the union of the local and remote groups. Processes should provide identical local_comm and local_leader arguments within each group. Wildcards are not permitted for remote_leader, local_leader, and tag.

In other words, if you provide two intra-communicators, a leader on each one and a bridge communicator where the leaders can talk together, you will be able to bind the two groups of processes corresponding to each of the intra-communicators into a inter-communicator. Neat! Graphically speaking this should look like
MPI_Intercomm_create

So far so good, but what “uniformly” means? Based on some web resources uniformly is about consistency, in this particular instance about the fact that all participants will return the same answer (aka. the some inter-communicator or the same error code) despite all odds. Here we are looking specifically from the point of view of process failures, more precisely a single failure. Obviously, the trivial approach where one agrees on the resulting intercomm doesn’t work, as due to process failures some processes might not have an intercomm. Clearly, we need a different, better approach.

While talking about this, Aurelien proposed the following solution, entirely based on MPI_Barrier.

Looks quite simple and straightforward. Does it do reach the expected consensus at the end? Unfortunately not, it doesn’t work in all cases. Imagine that all peers in one side succeeded to create the intercomm while everyone in the remote communicator failed. Then on one side the interexists is TRUE while on the other side it is FALSE. Thus the local barrier (line 3) succeed on the side with interexists equal to TRUE and the intercomm is not revoked. As the intercomm exists, these processes will then go in the second MPI_Barrier (line 10), on the “half-created” intercomm, and will deadlock as there will never be a remote process to participate to the barrier.

What we are missing here is an agreement between the two sides (A and B) that things went well for everyone. So let’s try to use agreement to reach this goal. In the remaining of this post I will use the function AGREE, which is a point-to-point agreement between two processes (the two leaders). We need this particular function, as we cannot call MPI_Comm_agree on the bridge communicator, simply because the two leaders are not the only participants in the bridge communicator. Fortunately, implementing an agreement between two processes is almost a trivial task, so I will consider the AGREE function as existing.

If there is no failure the code works, but it’s an overkill. Now, if we have one failure during the execution there are several cases.
1. The failure happens before the MPI_Intercomm_create. Some processes will have an intercomm, and some will not. Thus the local agreement will make everyone on the same group (A and B) agree about the local existence of the intercomm. The AGREE between the leaders will then propagate this knowledge to the remote group leader. At this point the two leaders have the correct answer, and then the MPI_Comm_agree at line 8 will finally distribute this answer on the two groups. This case works!
2. The failure happen after the MPI_Intercomm_create. One can think about this case as a false positive (because the intercomm exists on all alive processes), but the real question is if we are able to detect it and reach a consensus. The MPI_Comm_agree at line 3 will make the flag TRUE on both groups. Note that on one side the MPI_Comm_agree will return MPI_ERR_PROC_FAILED as required by the MPI standard, but we do not take in account the return code here.

Here is the reasoning leading to this form of the algorithm.
1. The MPI_Comm_agree on line 3 is a little tricky. We use the returned value of the flag (bitwise AND operation between all living processes), but we willingly choose to ignore the return value. What really matters is that all alive participants have the resulting intercomm, and this will be reflected in the value of flag after the call. All other cases are trapped either by partially existing intercomm, or by the REVOKE call. Moreover, it is extremely important that the resulting value of flag is computed through an agreement and not through a traditional collective communication (which lack the consistency factor).
2. For a similar reason the MPI_Comm_agree on line 9 cannot be replaced by a MPI_Broadcast, even as its meaning is to broadcast the information collected at the local root into the local group of processes. Without the use of MPI_Comm_agree here one cannot distinguish between every process still alive has an intercomm with known faults or only some participants have an intercomm (with faults). Thus, as the intercomm can be revoked only if all alive processes know about it, we have to enforce this consistent view by the use of the agreement.

While this inter-communicator creation looks like an extremely complicated and expensive matter, one should keep in mind that such communicator creation are not supposed to be in the critical path, so they might not be as prohibitive as one might think. If Everything Was Easy Nothing Would Be Worth It!