Tips, Tricks, Todos and Troubleshooting

Tips, Tricks, Todos and Troubleshooting#

With no particular order, we draw hereafter a list of questions that may come to the user’s mind. This list will be updated according to the users’ feedback.

How do I add a new parameter to a setup ?#

Imagine you want to add a real variable RHOR (density on the right side) to the set up sod1d (thus far the right value of the density in the Riemann problem is hard-coded in condinit.c). Just add a line such as the following in setups/sod1d/sod1d.par:

RhoR            0.1

and this is all. A python script which parses this file makes sure that you have access to a global real variable named RHOR throughout all the functions of the C code. You can now use this variable to replace the hard-coded value in setups/sod1d/condinit.c.

Note

The variable name in the .par file is case insensitive, but C is case sensitive. The name is converted to upper case for the C code. You must help the parser to automagically guess the type of the variable. Here “0.1” works, but “.1” would not.

How do I create a new Field variable?#

  1. Create a pointer in src/global.h.

    Example: Field *Myfield;

  2. Allocate memory with the function CreateField(). To do that, in src/LowTasks.c, inside the function CreateFields(), add:

    Myfield = CreateField("myfield",0,0,0,0);

Note

When using the new field inside a function/kernel, do not forget the corresponding INPUT/OUTPUT statements.

How do I write a Field?#

To write the Field myField in the disk, add

__WriteField(Myfield, TimeStep);

in src/output.c, inside the function WriteOutputs().

What is the way to merge the outputs of a run spawned with the -k flag ?#

Spawning a run with the -k flag keeps one output file per processor (for a given variable) instead of merging these files to produce a unique, larger file.

Assume you run ran on 8 processors, and you want to merge the output #5. You may issue on the command line, in FARGO3D’s main directory:

mpirun -np 8 ./fargo3d -s 5 -0 yourparfile

It will do the trick (restart from fragmented output -lower s-, then merge outputs, and exit). Edit the above line according to your needs, or insert it into a bash loop to merge the outputs of an entire directory.

Note

This technique is non-destructive, in the sense that it does neither change nor remove the individual outputs.

Warning

The above instruction requires that the whole simulation may fit on your platform’s memory. If you issue it on a small laptop for a simulation that ran on a large cluster, it may fail if there is not enough RAM.

I see lots of “!” or “:” instead of “.” at execution. What does that mean?#

This happens when you have a GPU built, and GPU-GPU communications are not fully optimized. See the section GPU/CPU communications and CUDA aware MPI implementations. Note that periodic boundary conditions are handled like normal MPI communications, even on a one process run, so that they transit through the host (CPU) if no CUDA aware version of MPI is used.

Where my last run data has been output ?#

The path to this directory is given by the parameter ‘OUTPUTDIR’ in the parameter file that you specified in your run. If this parameter begins with a ‘@’, this character should be substituted with the content of the FARGO_OUT environment variable, if it exists. You can also go to your home directory. There, a directory name .fargo3drc has been produced, which contains two files: history and lastout. The latter contains for each run issued a timestamp and the path to the output directory. The former contains a timestamp, the command that was issued to run the code, the number of processes, the list of hosts (and devices for GPU builts) on which the code was run, and the output directory. The lastout file is obsolete. You may define an alias in your .bashrc file that brings you automatically to the last output directory:

alias fo='cd `tail -n 1 $HOME/.fargo3drc/history`'

My build produces unexpected results. Some files should have been remade and they have not. How do I fix this ?#

Although we have dedicated some care to the chain of rules of the relatively complex build process, we may have failed to respect some dependencies. If you believe that your make process is flawed, the simplest solution is to note your build options with make info, then issue a make mrproper and finally rebuild by issuing a new make command followed by all your build options.

My code does not run much faster on the GPU than on the CPU. Why is this ?#

There are several reasons for this.

  • Your setup is very small, and your GPU(s) is/are underused.

  • You have default block sizes in your .opt file that are far from optimal, yielding a degradation of performance.

  • You have a high end CPU and a low end GPU…

  • You may not have tuned sufficiently the GPU build options in src/makefile. Make sure to set them to your target GPU architecture.

  • You have a 2D, YZ setup (see the note below about reductions).

Warning

Reductions are operations on a whole mesh that amount to obtaining a single number as a function of all cells’ content (hence the name “reduction”). It may be the sum of the mass or momentum content of all cells, or the minimum of all time steps allowed on all cells as a result of the CFL criterion: the reduction operation can be a sum, a min(), etc. We see that there is at least one unavoidable reduction operation per time step: the search for the maximum time step allowed. Reduction operations are performed in a two stage process:

  • A reduction in the X direction, at the end of which we obtain a 2D array in YZ. This reduction is performed on board the GPU, using the algorithm described in this pdf document. This corresponds to one of the few kernels that are written explicitly in FARGO3D (instead of being produced by the Python script). The user should never have to interfere with it.

  • A further reduction in the Y an Z dimensions of the previous 2D array. This is done on the host, as this has a low computational cost. This operation involves a Device->Host communication only, of a one cell thick single 2D array, which is not taken into account when evaluating 2D communications that yield the “:” diagnostic on the terminal (see CUDA aware MPI implementations).

The two stage process detailed above is generally not a problem, as we expect most setups to have a number of zones in X (or azimuth) much larger than the GPU vs CPU speed up factor (hence it is the first stage -reduction on board of the GPU- that constitutes the time consuming part). If however you have a YZ setup, the number of zones in X is just one, and in this case it is the second stage of the reduction process (on board the CPU) that constitutes the bottleneck: it is like if the reduction was entirely performed on the CPU. If you want to assess how much of your setup’s slowness can be put on the account of this restriction, you may try to hard-code the time step in src/algogas.c to see if this yields significant improvement. Also, during this test, you have to deactivate all monitoring in the .opt file, as monitoring requires reductions which are performed as described above.

What is this @ sign at the beginning of the outputs’ path ?#

Unless you have defined the environment variable FARGO_OUT, this “@” sign is not used, and you may remove it if you wish. When the FARGO_OUT environment variable is defined (for instance in your job script or in your .bashrc file), its value substitutes the “@” sign in your output path. If, for instance, you have:

OutputDir   @mri/beta150

in your .par file, and you have defined in your .bashrc file the following:

export FARGO_OUT='/data/myname/fargo3d'

then your run will output its data in /data/myname/fargo3d/mri/beta150.

This trick is version control friendly: you define once for ever the sub directory where you want your data to be, and the prefix part is specified in the environment variable out of the version control, so that if different persons work on the parameter file, it will not trigger a sequence of different versions. You may have on one platform:

export FARGO_OUT='/data2/pablo/fargo3d'

and on another one:

export FARGO_OUT='/scratch3/frederic/fargo3d'

and the same parameter file may be used without any editing.

I see that there are .par files in each setup directory, and the same .par files are found in the in/ sub directory. What is this for ?#

The .par files found in the setup directories are necessary to build FARGO3D: a python script uses them to determine the set of global upper case variables that will be available everywhere throughout the C code, with the value that the user defines for them in his .par file. Therefore, these “setup” or “master”.par files must include all variables that can ever be used by the setup, and they must specify default, fiducial values for all parameters.

Although the user may run the code by using these “master” parameter files, e.g.:

./fargo3d setups/fargo/fargo.par

this is not customary and any other parameter file, with different parameter values than those specified in the “master” parfile, may be used:

./fargo3d in/fargo.par

You may have a large set of parameters files with different values, and you can run the code on them without any rebuild.

Note

If a parameter is not defined in a parameter file, the code will take its default value from the “master” parameter file, unless this parameter is specified as mandatory, in which case the user must specify its value in any parameter file (otherwise an error message is issued and the code stops.)

Warning

It is recommended to edit the parameter files of the in/ directory, rather than interfering with the “master” parameter files found in the setups directories.

See also

Defining the parameter file.

I have noticed a directory named .fargo3drc in my home directory. What is it here for ?#

This directory contains two text files (history and lastout) which are updated at each new run. Every time a new run is spawned, two lines are appended to the history file: a line indicating the date and time at which the run was launched, and the command line issued to launch the run. In addition, two new lines are appended to the lastout file: a time stamp as previously, and the absolute path of the output directory. It can be useful to parse the last line of this file with a script to go directly where the output is written:

alias fo='cd `tail -n 1 $HOME/.fargo3drc/lastout`'

The above line, in the .bashrc file, will define a command fo (like Fargo3d Output) which changes the directory to the output directory of the last run.

Known issue:

When the -o flag is used on the command line, the subsequent quotation marks are not written to the file history. If one wishes to cut and paste some line of this file to repeat a given run, one must ensure to manually edit the line to restore the quotation marks, when the flag -o is used.

How can I see the output of python scripts (in particular the CUDA files) ?#

You will find below information to retrieve manually the output of each of the python scripts involved at build stage. However, starting from version 1.3, the build process creates an arch/ subdirectory in which all the source files are archived, even those created automatically such as those created by the boundary conditions scripts or the c2cuda converter. It is therefore much easier than in earlier versions to have a glance at the intermediate source files automatically created at build time.

You may have noticed a long list of files being removed at the end of the build process, especially on GPU builds. These files are intermediate files such as CUDA files automatically produced by the c2cuda script, etc. and the make process must remove them upon completion in order to preserve dependencies. Failing to do so would result, for instance, in the GPU version of a routine not being rebuilt if its C source was edited. We do not issue explicitly this rm command in the makefile. This is done automatically, out of our control, because make knows that it must preserve dependencies.

This may be frustrating as you cannot have a look at the CUDA files or boundary source codes produced by the Python scripts. This, sometimes, can be useful to understand unexpected behaviors. Here we indicate the manual procedure to produce all the intermediary files used during the build process. Do not forget to remove them prior to a full build of the code, or dependencies may be broken !

Creation of var.c:

In src/, issue:

python ../scripts/par.py ../setups/mri/mri.par ../std/stdpar.par

Naturally substitute the mri setup in the above line with your own setup.

Creation of param.h, param_noex.h, global_ex.h:

In src/, issue:

python ../scripts/varparser.py

Creation of rescale.c:

In src/, issue:

python ../scripts/unitparser.py mri

The rescale.c file is produced in the src directory

Creation of boundary source code:

In src/, issue:

python ../scripts/boundparser.py ../std/boundaries.txt  ../std/centering.txt ../setups/mri/mri.bound

If you issue the command ls -ltr you will see new files with name [y/z][min/max]_bound.c that you can examine. Note that since periodic boundary conditions are not dealt with as other BCs but rather with communications, they do not generate such files. For instance, with the mri setup, you only have the y files, not the z files.

Creation of the CUDA source code:

It can be done for any of the files which has same radix than those of the list GPU_OBJBLOCKS in the makefile. We take the example here of the file compute_emf.c. In the src/ directory, issue:

python ../scripts/c2cuda.py -i compute_emf.c -o foo.cu

In this command line, -i stands for the input, and -o for the output. Note that we do not follow here the automatic rule that would create ../bin/compute_emf_gpu.o. As a result, there is no risk to break dependencies if we forget to remove the file created manually. You can examine the file foo.cu and compare it to the input C file. You may also try to invoke it with the -p flag that implements a loop in the wrapper function to determine the best block size.

Tweaking the CUDA executable for memory optimization#

The default behavior of memory allocation on the GPU is to pad arrays in order to respect the alignment of all rows. This may consume an extra amount of memory, which is very parameter dependent. If you wish to allocate memory like on the host, without padding, you may use the compilation flag NOPITCH (e.g. in the opt file, add the following line: FARGO_OPT += -DNOPITCH', and rebuild). The performance degradation is negligible and you may be able to use slightly larger arrays on a given GPU.

Speeding up reduction operations on platform >= 3.5#

Reductions are by default implemented as described on a famous presentation by Mark Harris (NVIDIA), which works for all platforms, even old ones. On >= 3.5 platforms, one may use the possibility of warp shuffle, which can significantly speed up reductions. In order to do that, you must use the compilation flag WARPSHUFFLE (e.g. in the opt file, add the following line: FARGO_OPT += -DWARPSHUFFLE', and rebuild). The new kernel thus called reduces the amount of shared memory used by the GPU. As described for standard reductions, the reduction thus executed is done along the X direction only, and the subsequent reduction in Y and Z is performed on the CPU.

A very incomplete TODO list#

We have several projects or improvements in mind for FARGO3D. Some of them are cosmetic time savers, others are more substantial. Among them:

  • Since we can parse the C code to produce CUDA code, we can also, in principle, produce automatically OpenCL code. This would enable FARGO3D to run on non-NVIDIA’s GPUs, and on multi-core platforms.

  • We would like to merge FARGO3D and the nested mesh structure of the code JUPITER (developed by one of us but never publicly released). This would require to have normal ghost zones in the X direction (as for Y and Z), a 3D mesh splitting of processing elements, and an adaptation of the ghost filling procedure. In this page you can see JUPITER at work with a number of nested meshes onto a giant planet.