Octopus can be used on large clusters and supercomputers, but to do this efficiently, it is important to understand how to judge the efficiency of its parallelization scheme. To achieve this, we will conduct a scaling analysis in this tutorial, for which we will run Octopus for a certain system with different numbers of processes and compare the timings. This kind of analysis is also called "strong scaling".
A code like octopus is parallelized to utilize more computing resources at the same time, thus reducing the time to solution for calculations. Naively, one could expect that using twice the number of CPU cores for a calculation should cut the time needed by a factor of two. However, not all parts of a program are typically running in parallel and also there is some overhead associated with the parallelization scheme itself, such as communication between processes. Hence, the time for the execution of a certain computation on processors will depend on the fraction of serial work because only the parallel fraction can be sped up by a factor of :
The speed-up is defined as the ratio . Plugging in the formula from above yields
This relation is called Amdahl's law. It means that the achievable speed-up can never be larger than the inverse of the serial fraction. If the serial fraction is 50%, the speed-up cannot be larger than 2; if the serial fraction is 10%, the speed-up cannot be larger than 10; if the serial fraction is 1%, the speed-up cannot be larger than 100. As you can see, the serial fraction must be very small to achieve large speed-ups: for achieving a speed-up of 10000, the serial fraction must be less than .
From this, it also follows that it one should not use more cores for a computation than the maximum speed-up that can be reached. If, for example, the maximum speed-up is 10, it does not make sense to run this calculation on 100 cores - this would be inefficient and waste resources.
To judge the efficiency of the parallelization, one can use the parallel efficiency which is defined as the ratio of the observed speed-up to the ideal speed-up, . As an example, when comparing a run on 4 cores to a run on 1 core, for which the speed-up is 3, the ideal speed-up would be 4 and thus the parallel efficiency is in this case. As a rule of thumb, efficiencies above 70% are acceptable.
In practice, one usually does not know the serial fraction. Thus, one executes the code for a short test case for several numbers of processes to obtain the speed-up, scaling curve, and efficiency. From this, one can then infer up to which point the parallelization is still efficient and one should choose this number of processors for subsequent runs to efficiently use the computing resources.
If in doubt, it is usually more efficient to use slightly less resources, but run several simulations at the same time (which is often required) - this will use the resources efficiently and still provide a small total time to solution because several calculations can run in parallel.
Be aware that on supercomputers, the available computing time is shared between the members of a project or between the members of a group. If everyone runs their code efficiently, the number of simulations that can be done by all members of the group is maximized and thus more papers can be produced!
Scaling analysis for domain parallelization
As a first example, we will do a strong scaling analysis for the same input as in the previous tutorial. Save the following as inp file:
CalculationMode = gs FromScratch = yes XYZCoordinates = "1ala.xyz" Spacing = 0.2*angstrom Radius = 4.0*angstrom TDPropagator = aetrs TDMaxSteps = 20 TDTimeStep = 0.05
and the following as "1ala.xyz":
23 units: A N -1.801560 0.333315 -1.308298 C -1.692266 1.069227 0.012602 C -0.217974 1.151372 0.425809 O 0.256888 2.203152 0.823267 C -2.459655 0.319513 1.077471 H -1.269452 0.827043 -2.046396 H -1.440148 -0.634968 -1.234255 H -2.791116 0.267637 -1.602373 H -2.104621 2.114111 -0.129280 H -2.391340 0.844513 2.046396 H -2.090378 -0.708889 1.234538 H -3.530691 0.246022 0.830204 N 0.476130 -0.012872 0.356408 C 1.893957 -0.046600 0.735408 C 2.681281 0.990593 -0.107455 O 3.486946 1.702127 0.516523 O 2.498931 1.021922 -1.333241 C 2.474208 -1.425485 0.459844 H 0.072921 -0.880981 0.005916 H 1.975132 0.211691 1.824463 H 1.936591 -2.203152 1.019733 H 3.530691 -1.461320 0.761975 H 2.422706 -1.683153 -0.610313
Then, run the ground state calculation or reuse the ground state from the previous tutorial. For running the calculations, you can use the batch scripts from the previous tutorial.
For this analysis, we will only look at the parallelization using MPI and disregard the OpenMP parallelization for the time being. Usually, these two components can be examined independent of each other, keeping the other fixed.
Baseline: serial run
As a baseline, we need to run the TD calculation on one processor. Change the CalculationMode variable to td and submit a batch script to execute it on one core. Check the parallelization section in the output and make sure that it is executed in serial.
From the output of the timestep information, you can again get an average of the elapsed time per timestep:
********************* Time-Dependent Simulation ********************** Iter Time Energy SC Steps Elapsed Time ********************************** ********************************** 1 0.050000 -109.463446 1 1.060 2 0.100000 -109.463446 1 1.093 3 0.150000 -109.463446 1 1.064 4 0.200000 -109.463446 1 1.032 5 0.250000 -109.463446 1 0.940 6 0.300000 -109.463446 1 0.957 7 0.350000 -109.463446 1 0.901 8 0.400000 -109.463446 1 0.860 9 0.450000 -109.463446 1 0.880 10 0.500000 -109.463446 1 0.958 11 0.550000 -109.463446 1 0.846 12 0.600000 -109.463446 1 0.855 13 0.650000 -109.463446 1 0.826 14 0.700000 -109.463446 1 0.805 15 0.750000 -109.463446 1 0.805 16 0.800000 -109.463446 1 0.832 17 0.850000 -109.463446 1 0.814 18 0.900000 -109.463446 1 0.788 19 0.950000 -109.463446 1 0.812 20 1.000000 -109.463446 1 0.897
In this case, the average of the 20 time steps would be about 0.90s.
To analyze the scaling, we will run TD calculations with a logarithmic spacing in the number of processors, using 2, 4, 8, and 16 cores. To make sure that domain parallelization is used, add the following to the inp file:
ParStates = 1 ParDomains = auto
Submit a job script with for each of the core numbers and wait until they are finished. Then, extract the average time for one time step as we did above for the serial run.
With these numbers, you can fill the following table:
The numbers you get from your own measurement can deviate, but overall the result should be similar.
Using the times you measured, compute the speed-up and the parallel efficiency as introduced earlier in the tutorial. You should get a table that is similar to the following:
What do these numbers tell us? First of all, the parallel efficiency is almost 80% when using 2 cores, so that is still fine. Going to more cores, the efficiency drops. Thus, for this system it is inefficient to use more than 2 cores for the domain parallelization.
A standard way of visualizing scaling data is to display a log-log plot of the speed-up vs. the number of cores. A little python script for doing this can be found at the end of the tutorial. When the speed-up is near the line of the ideal speed-up, the efficiency is good, but once it drops below, the scaling breaks down.
Why does the efficiency drop for more than 2 cores? As you might remember from the previous tutorial on parallelization, the parallelization in domains is only efficient, when the number of inner points is large enough compared to the number of ghost points. So let's compare the ratio of ghost points to local points, which should be less than about 25% as a rule of thumb. For this, you need to look at the information on the mesh partitioning, which should look similar to the following on 2 cores:
Partition quality: 0.244738E-08 Neighbours Ghost points Average : 1 14293 Minimum : 1 14150 Maximum : 1 14435 Nodes in domain-group 1 Neighbours : 1 Local points : 70175 Ghost points : 14435 Boundary points : 27217 Nodes in domain-group 2 Neighbours : 1 Local points : 70154 Ghost points : 14150 Boundary points : 27859
For this case, the ratio would be about 14435/70175=21%.
What are the ratios you get for the other core numbers? Can they explain the drop in efficiency?
(as a reference, the ratios should be roughly: 2 cores: 21%; 4: 35%; 8: up to 70% 16: up to 111%)
Scaling analysis for states parallelization
Let's do a similar analysis, but for states parallelization. Change the parallelization options to
ParStates = auto ParDomains = 1
to make sure only states parallelization is used. Then submit batch jobs to run the code on 1, 2, 4, 8, and 16 cores. Gather the timings as in the previous section and create a table of the timings; also compute the speed-up and parallel efficiency for all runs. The table should be similar to (the timings can vary, but the speed-up and efficiency should be similar):
As one can see, the efficiency is above 70% only up to 4 cores; above the efficiency drops. Thus, for this system, state parallelization should only used up to 4 cores.
Now the question is: why does the scaling break down above 4 processes and especially above 8 processes? Let's look at the parallelization output from the log of the 8-core run:
Info: Parallelization in states Info: Node in group 0 will manage 4 states: 1 - 4 Info: Node in group 1 will manage 4 states: 5 - 8 Info: Node in group 2 will manage 4 states: 9 - 12 Info: Node in group 3 will manage 4 states: 13 - 16 Info: Node in group 4 will manage 4 states: 17 - 20 Info: Node in group 5 will manage 4 states: 21 - 24 Info: Node in group 6 will manage 4 states: 25 - 28 Info: Node in group 7 will manage 4 states: 29 - 32
The system has 32 states, thus each core processes 4 states. In the previous tutorial, it was indicated as a rule of thumb that 4 states per process is the minimum to be efficient, also in terms of vectorization. As one can see, the calculation time does not even decrease when going to 16 cores, where each core processes only 2 states. However, on 4 cores, each process has 8 states and that is more efficient.
Combined states and domain parallelization
Now run the system again, combining states and domain parallelization, with 2 cores each and with 2 and 4 cores. Extract the timings and compute the speed-up and parallel efficiency. What is the most efficient way to run this system?
We don't treat k-point parallelization in detail here, because it is only relevant for solids which are covered in a later tutorial. But as the parallelization is quite trivial, you can scale the processes up to using only 1 k point per process. It is most efficient when the distribution of k points to processes is balanced (e.g. all cores have 2 k-points instead of some having 2 and some having only 1).
Usually, production runs are larger and require more resources. Thus, one usually requests full nodes and then the scaling analysis is done using 1, 2, 4, 8, ... full nodes and the speed-up is computed relative to one node. Other than that, the analysis is the same as outlined above.
For one of the systems you use in production runs: how many cores or nodes do you usually use? Is that efficient? Run a quick scaling analysis on 3 or 4 different node counts to estimate the parallel efficiency. Check the guidelines for the different parallelization strategies.
Another reason to use more nodes besides the larger compute power is the larger memory that might be needed. If the memory needed for the states is too large to fit into the main memory of one node, more nodes need to be used to distribute the storage of the states across nodes.
There is a section in the output that gives approximate memory requirements. For the example from the previous sections, it looks as follows:
****************** Approximate memory requirements ******************* Mesh global : 2.9 MiB local : 7.4 MiB total : 10.3 MiB States real : 47.1 MiB (par_kpoints + par_states + par_domains) complex : 94.1 MiB (par_kpoints + par_states + par_domains) **********************************************************************
This indicates that mesh object takes about 10 MiB on each core and that the states in total require 94 MiB for complex numbers (which are used for TD runs). To estimate the total amount of memory needed, one can add the memory for the states to the memory of mesh times the number of processes because the mesh information is needed on each process. If this is larger than the memory per node (which can usually be found in the documentation of the corresponding cluster or supercomputer), one can estimate the number of nodes needed by dividing the total memory needed by the memory per node.
Sometimes, supercomputers also offer compute nodes with more memory per node, then it can also be an option to request those nodes.
Here is a brief summary of guidelines:
- do a scaling run for new systems and compute parallel efficiency
- parallel efficiency should be >70%
- in doubt use less cores and run several simulations in parallel
- for states parallelization: minimum 4-8 states per core
- for domain parallelization: ratio ghost/local points should be <25%
- for k-point parallelization: up to 1 k point per core
- for k-point and states parallelization: a balanced distribution is more efficient
- do not waste resources; leads to more science being done by all!
You can use the following python script to create a scaling plot as a log-log plot of speed-up vs. core number:
import numpy as np import matplotlib.pyplot as plt from matplotlib.ticker import NullFormatter # number of cores cores = np.array([1, 2, 4, 8, 16]) # enter the times you measured here times = np.array([0.90, 0.57, 0.34, 0.21, 0.11]) speedup = times/times ideal_speedup = cores/cores plt.loglog(cores, speedup, label="speed-up") plt.loglog(cores, ideal_speedup, label="ideal") plt.xlabel("Cores") plt.ylabel("Speed-up") plt.legend() # some formatting plt.gca().set_xticks(cores) plt.gca().set_xticklabels(cores) plt.gca().set_yticks(cores) plt.gca().set_yticklabels(cores) plt.gca().xaxis.set_tick_params(which='minor', size=0) plt.gca().yaxis.set_tick_params(which='minor', size=0) plt.savefig("speedup.pdf")