Documentation of the profiling examples

examples/profiling/README.md

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+Standardized profiling setups for i-PI
+======================================
+
+This folder contains a few inputs designed to stress-test the i-PI implementation, and determine internal bottlenecks.
+To emphasize the overhead associated with the Python implementation and the socket communication, these examples 
+use dummy drivers that do not compute actual forces, or skip altogether the force evaluation.
+
+The inputs provided are for very small systems with 8 atoms (so the focus is on the constant overhead of the simulation)
+but it's possible to perform runs with an arbitrary number of atoms using `run_profiling.sh natoms`.
+The -p option activates wall-clock-time profiling using `yappi`.
+
+Examples include:
+
+`classical_md_gas` runs a simple NVE dynamics using an ideal-gas driver
+
+`classical_md_noff` runs a simple NVE dynamics. sets force weights to zero so there is no forcefield evaluation
+
+`remd_scpimd_gas` runs a super-duper calculation with replica exchange, constant-pressure NpT ensemble and Suzuki-Chin high-order path integrals
+
+`remd_scpimd_noff` as above, but without forcefield 

examples/profiling/classical_md_gas/input.xml

@@ -1,4 +1,4 @@
-<simulation verbosity='medium' threading='false' safe_stride='100'>
+<simulation verbosity='low' threading='false' safe_stride='100'>
     <ffsocket mode='unix' name='driver' pbc='false'>
          <latency>  1.00000000e-04</latency>
          <address> gas </address>

examples/profiling/remd_scpimd_gas/init.xyz

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+8
+# CELL(abcABC):   50.0 50.0 50.0 90.00000    90.00000    90.00000  
+H 0 0 0
+H 0 0 1
+H 0 0 2
+H 0 0 3
+H 0 0 4
+H 0 0 5
+H 0 0 6
+H 0 0 7

examples/profiling/remd_scpimd_gas/input.xml

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+<simulation verbosity='low' threading='true' safe_stride='100'>
+    <ffsocket mode='unix' name='dummy.1' pbc='false'>
+         <latency>  1.00000000e-04</latency>
+         <address> gas </address>
+         <exit_on_disconnect> False </exit_on_disconnect>
+   </ffsocket>
+    <fflj name='dummy.2' pbc='False'>
+      <parameters>{eps: 0.0, sigma: 1.0}</parameters>
+   </fflj>
+   <total_steps>2000</total_steps>
+   <output prefix='simulation'>
+      <trajectory stride='2000' filename='pos'> positions </trajectory>
+      <properties stride='2000'> [ step, time, conserved, temperature, kinetic_md, potential, pressure_md, volume ] </properties>
+   </output>
+   <prng>
+      <seed>18885</seed>
+   </prng>
+  <system_template>
+     <labels>   [ PREFIX, FILENAME, TEMPERATURE, PRESSURE ] </labels> 
+     <instance> [ REF00, init.xyz, 300, 1 ] </instance>
+     <instance> [ REF01, init.xyz, 310, 1 ] </instance>
+     <instance> [ REF02, init.xyz, 320, 1 ] </instance>
+     <instance> [ REF10, init.xyz, 300, 10 ] </instance>
+     <instance> [ REF11, init.xyz, 310, 10 ] </instance>
+     <instance> [ REF12, init.xyz, 320, 10 ] </instance>
+     <template>          
+          <system prefix="PREFIX">
+            <initialize nbeads="4">
+              <file mode="xyz"> FILENAME </file>
+              <cell> [10.0, 0, 0, 0, 10.0, 0, 0, 0, 10.0] </cell>
+              <masses mode='manual'> [1.0] </masses>
+              <velocities mode="thermal" units="kelvin"> TEMPERATURE </velocities>
+            </initialize>
+            <forces>
+              <force forcefield ="dummy.1"  weight='1.0'/>
+              <force forcefield ="dummy.2"  nbeads='2' weight='1.0'/>
+            </forces>
+            <motion mode="dynamics">
+              <dynamics mode="scnpt">
+                <barostat mode='sc-isotropic'>
+                  <tau units='femtosecond'> 200</tau>
+                  <thermostat mode='langevin'>
+                    <tau units='femtosecond'> 100</tau>
+                  </thermostat>
+                  <h0> [ 32.84024, 0, 0, 0, 32.84024, 0, 0, 0, 32.84024 ]</h0>
+                </barostat>
+                <thermostat mode='langevin'>
+                  <tau units='femtosecond'> 100 </tau>
+                </thermostat>
+                <timestep units="femtosecond"> 1.0 </timestep>
+              </dynamics>
+            </motion>
+            <ensemble>
+              <temperature units="kelvin"> TEMPERATURE </temperature>
+              <pressure units="megapascal"> PRESSURE </pressure>
+              <bias> <force forcefield="dummy.2"/> </bias>
+              <bias_weights> [0.0] </bias_weights>
+            </ensemble>
+          </system>
+  </template>
+  </system_template>
+  <smotion mode="remd">
+    <remd>
+      <stride> 2 </stride>
+    </remd>
+  </smotion>
+</simulation>

examples/profiling/remd_scpimd_noff/input.xml

@@ -1,4 +1,4 @@
-<simulation verbosity='medium' threading='true' safe_stride='100'>
+<simulation verbosity='low' threading='true' safe_stride='100'>
     <fflj name='dummy.1' pbc='False'>
       <parameters>{eps: 0.0, sigma: 1.0}</parameters>
    </fflj>
@@ -25,6 +25,8 @@
           <system prefix="PREFIX">
             <initialize nbeads="4">
               <file mode="xyz"> FILENAME </file>
+              <cell> [10.0, 0, 0, 0, 10.0, 0, 0, 0, 10.0] </cell>
+              <masses mode='manual'> [1.0] </masses>
               <velocities mode="thermal" units="kelvin"> TEMPERATURE </velocities>
             </initialize>
             <forces>

examples/profiling/run_profiling.sh

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+#!/bin/bash
+# usage: run_profile.sh [-p] natoms
+# run a mock simulation using an natoms box, -p activates yappi profiling
+
+# Default value for natoms
+natoms=8
+# Default profiler options
+profiler_options=""
+
+# Process command-line arguments
+while getopts ":p" opt; do
+  case $opt in
+    p)
+      profiler_flag=true
+      ;;
+    \?)
+      echo "Invalid option: -$OPTARG" >&2
+      ;;
+  esac
+done
+shift $((OPTIND-1))
+
+# Set natoms if provided as an argument
+if [ $# -gt 0 ]; then
+    natoms=$1
+fi
+
+# Set profiler options if -p flag was used
+if [ "$profiler_flag" = true ]; then
+    profiler_options="-p --profiler-clock=wall --profiler-output=test-$natoms"
+fi
+
+# Create test.xyz file
+echo $natoms > test-$natoms.xyz
+echo "# dummy input structure" >> test-$natoms.xyz
+for (( i=0; i<natoms; i++ ))
+do
+    echo "H 0 0 0" >> test-$natoms.xyz
+done
+
+# Replace init.xyz with test.xyz in input.xml and save as test.xml
+sed 's/init\.xyz/test-'$natoms'\.xyz/g' input.xml > test-$natoms.xml
+
+# Run i-pi and i-pi-driver in the background
+time i-pi test-$natoms.xml $profiler_options &> test-$natoms.log &
+sleep 1
+i-pi-driver -m gas -u -a gas &
+
+# Wait for all background processes to finish
+wait
+