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2025.2
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CPU nodes
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A100 nodes
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GH nodes
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2025.3
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CPU nodes
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A100 nodes
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GH nodes
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SBATCH CPU, 4 MPI ranks, 16 OMP threads
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SBATCH A100, 4 GPU, 16 OMP threads, 4 MPI ranks
</span>
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<a href="#sbatch-gh-2-gpu-18-omp-threads-2-mpi-ranks" class="md-nav__link">
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SBATCH GH, 2 GPU, 18 OMP threads, 2 MPI ranks
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M10 20H6V4h7v5h5v3.1l2-2V8l-6-6H6c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h4zm10.2-7c.1 0 .3.1.4.2l1.3 1.3c.2.2.2.6 0 .8l-1 1-2.1-2.1 1-1c.1-.1.2-.2.4-.2m0 3.9L14.1 23H12v-2.1l6.1-6.1z"></path></svg>
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<h1 id="gromacs">GROMACS<a class="headerlink" href="#gromacs" title="Permanent link"></a></h1>
<h2 id="gromacs_1">GROMACS<a class="headerlink" href="#gromacs_1" title="Permanent link"></a></h2>
<p>GROMACS (GROningen Machine for Chemical Simulations) is a versatile and widely-used open source package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.</p>
<p>It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.)</p>
<h2 id="licensing-terms-and-conditions">Licensing Terms and Conditions<a class="headerlink" href="#licensing-terms-and-conditions" title="Permanent link"></a></h2>
<p>GROMACS is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software (see GROMACS Homepage for details).</p>
<h2 id="how-to-run-on-merlin7">How to run on Merlin7<a class="headerlink" href="#how-to-run-on-merlin7" title="Permanent link"></a></h2>
<h2 id="20252">2025.2<a class="headerlink" href="#20252" title="Permanent link"></a></h2>
<h3 id="cpu-nodes">CPU nodes<a class="headerlink" href="#cpu-nodes" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-0-2"><a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.7-ax23-A100-gpu<span class="w"> </span>gromacs/2025.2-whcq-omp
</span></code></pre></div>
<h3 id="a100-nodes">A100 nodes<a class="headerlink" href="#a100-nodes" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-1-2"><a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.7-3vzj-A100-gpu<span class="w"> </span>gromacs/2025.2-vbj4-A100-gpu-omp
</span></code></pre></div>
<h3 id="gh-nodes">GH nodes<a class="headerlink" href="#gh-nodes" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.7-blxc-GH200-gpu<span class="w"> </span>gromacs/2025.2-cjnq-GH200-gpu-omp
</span></code></pre></div>
<h2 id="20253">2025.3<a class="headerlink" href="#20253" title="Permanent link"></a></h2>
<h3 id="cpu-nodes_1">CPU nodes<a class="headerlink" href="#cpu-nodes_1" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.9-n4yf-A100-gpu<span class="w"> </span>gromacs/2025.3-6ken-omp
</span></code></pre></div>
<h3 id="a100-nodes_1">A100 nodes<a class="headerlink" href="#a100-nodes_1" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-4-2"><a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.9-xqhy-A100-gpu<span class="w"> </span>gromacs/2025.3-ohlj-A100-gpu-omp
</span></code></pre></div>
<h3 id="gh-nodes_1">GH nodes<a class="headerlink" href="#gh-nodes_1" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-5-1"><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-5-2"><a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.9-inxi-GH200-gpu<span class="w"> </span>gromacs/2025.3-yqlu-GH200-gpu-omp
</span></code></pre></div>
<h3 id="sbatch-cpu-4-mpi-ranks-16-omp-threads">SBATCH CPU, 4 MPI ranks, 16 OMP threads<a class="headerlink" href="#sbatch-cpu-4-mpi-ranks-16-omp-threads" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-6-1"><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="ch">#!/bin/bash</span>
</span><span id="__span-6-2"><a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="c1">#SBATCH --time=00:10:00 # maximum execution time of 10 minutes</span>
</span><span id="__span-6-3"><a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="c1">#SBATCH --nodes=1 # requesting 1 compute node</span>
</span><span id="__span-6-4"><a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="c1">#SBATCH --ntasks=4 # use 4 MPI rank (task)</span>
</span><span id="__span-6-5"><a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="c1">#SBATCH --partition=hourly</span>
</span><span id="__span-6-6"><a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="c1">#SBATCH --cpus-per-task=16 # modify this number of CPU cores per MPI task</span>
</span><span id="__span-6-7"><a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="c1">#SBATCH --output=_scheduler-stdout.txt</span>
</span><span id="__span-6-8"><a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="c1">#SBATCH --error=_scheduler-stderr.txt</span>
</span><span id="__span-6-9"><a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a>
</span><span id="__span-6-10"><a id="__codelineno-6-10" name="__codelineno-6-10" href="#__codelineno-6-10"></a><span class="nb">unset</span><span class="w"> </span>PMODULES_ENV
</span><span id="__span-6-11"><a id="__codelineno-6-11" name="__codelineno-6-11" href="#__codelineno-6-11"></a>module<span class="w"> </span>purge
</span><span id="__span-6-12"><a id="__codelineno-6-12" name="__codelineno-6-12" href="#__codelineno-6-12"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-6-13"><a id="__codelineno-6-13" name="__codelineno-6-13" href="#__codelineno-6-13"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.7-ax23-A100-gpu<span class="w"> </span>gromacs/2025.2-whcq-omp
</span><span id="__span-6-14"><a id="__codelineno-6-14" name="__codelineno-6-14" href="#__codelineno-6-14"></a>
</span><span id="__span-6-15"><a id="__codelineno-6-15" name="__codelineno-6-15" href="#__codelineno-6-15"></a><span class="nb">export</span><span class="w"> </span><span class="nv">FI_CXI_RX_MATCH_MODE</span><span class="o">=</span>software
</span><span id="__span-6-16"><a id="__codelineno-6-16" name="__codelineno-6-16" href="#__codelineno-6-16"></a>
</span><span id="__span-6-17"><a id="__codelineno-6-17" name="__codelineno-6-17" href="#__codelineno-6-17"></a><span class="c1"># Add your input (tpr) file in the command below</span>
</span><span id="__span-6-18"><a id="__codelineno-6-18" name="__codelineno-6-18" href="#__codelineno-6-18"></a>srun<span class="w"> </span>gmx_mpi<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>step6.0_minimization.mdp<span class="w"> </span>-o<span class="w"> </span>step6.0_minimization.tpr<span class="w"> </span>-c<span class="w"> </span>step5_input.gro<span class="w"> </span>-r<span class="w"> </span>step5_input.gro<span class="w"> </span>-p<span class="w"> </span>topol.top<span class="w"> </span>-n<span class="w"> </span>index.ndx
</span><span id="__span-6-19"><a id="__codelineno-6-19" name="__codelineno-6-19" href="#__codelineno-6-19"></a>srun<span class="w"> </span>gmx_mpi<span class="w"> </span>mdrun<span class="w"> </span>-s<span class="w"> </span>step6.0_minimization.tpr<span class="w"> </span>-pin<span class="w"> </span>on<span class="w"> </span>-ntomp<span class="w"> </span><span class="si">${</span><span class="nv">SLURM_CPUS_PER_TASK</span><span class="si">}</span>
</span></code></pre></div>
<h3 id="sbatch-a100-4-gpu-16-omp-threads-4-mpi-ranks">SBATCH A100, 4 GPU, 16 OMP threads, 4 MPI ranks<a class="headerlink" href="#sbatch-a100-4-gpu-16-omp-threads-4-mpi-ranks" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-7-1"><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="ch">#!/bin/bash</span>
</span><span id="__span-7-2"><a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a><span class="c1">#SBATCH --time=00:10:00 # maximum execution time of 10 minutes</span>
</span><span id="__span-7-3"><a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="c1">#SBATCH --output=_scheduler-stdout.txt</span>
</span><span id="__span-7-4"><a id="__codelineno-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></a><span class="c1">#SBATCH --error=_scheduler-stderr.txt</span>
</span><span id="__span-7-5"><a id="__codelineno-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></a><span class="c1">#SBATCH --nodes=1 # number of GH200 nodes with each node having 4 CPU+GPU</span>
</span><span id="__span-7-6"><a id="__codelineno-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></a><span class="c1">#SBATCH --ntasks-per-node=4 # 4 MPI ranks per node</span>
</span><span id="__span-7-7"><a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a><span class="c1">#SBATCH --cpus-per-task=16 # 16 OMP threads per MPI rank</span>
</span><span id="__span-7-8"><a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a><span class="c1">#SBATCH --cluster=gmerlin7</span>
</span><span id="__span-7-9"><a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a><span class="c1">#SBATCH --hint=nomultithread</span>
</span><span id="__span-7-10"><a id="__codelineno-7-10" name="__codelineno-7-10" href="#__codelineno-7-10"></a><span class="c1">#SBATCH --partition=a100-hourly</span>
</span><span id="__span-7-11"><a id="__codelineno-7-11" name="__codelineno-7-11" href="#__codelineno-7-11"></a><span class="c1">#SBATCH --gpus=4</span>
</span><span id="__span-7-12"><a id="__codelineno-7-12" name="__codelineno-7-12" href="#__codelineno-7-12"></a>
</span><span id="__span-7-13"><a id="__codelineno-7-13" name="__codelineno-7-13" href="#__codelineno-7-13"></a><span class="nb">unset</span><span class="w"> </span>PMODULES_ENV
</span><span id="__span-7-14"><a id="__codelineno-7-14" name="__codelineno-7-14" href="#__codelineno-7-14"></a>module<span class="w"> </span>purge
</span><span id="__span-7-15"><a id="__codelineno-7-15" name="__codelineno-7-15" href="#__codelineno-7-15"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-7-16"><a id="__codelineno-7-16" name="__codelineno-7-16" href="#__codelineno-7-16"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.7-3vzj-A100-gpu<span class="w"> </span>gromacs/2025.2-vbj4-A100-gpu-omp
</span><span id="__span-7-17"><a id="__codelineno-7-17" name="__codelineno-7-17" href="#__codelineno-7-17"></a>
</span><span id="__span-7-18"><a id="__codelineno-7-18" name="__codelineno-7-18" href="#__codelineno-7-18"></a><span class="nb">export</span><span class="w"> </span><span class="nv">FI_CXI_RX_MATCH_MODE</span><span class="o">=</span>software
</span><span id="__span-7-19"><a id="__codelineno-7-19" name="__codelineno-7-19" href="#__codelineno-7-19"></a>
</span><span id="__span-7-20"><a id="__codelineno-7-20" name="__codelineno-7-20" href="#__codelineno-7-20"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_GPU_DD_COMMS</span><span class="o">=</span><span class="nb">true</span>
</span><span id="__span-7-21"><a id="__codelineno-7-21" name="__codelineno-7-21" href="#__codelineno-7-21"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_GPU_PME_PP_COMMS</span><span class="o">=</span><span class="nb">true</span>
</span><span id="__span-7-22"><a id="__codelineno-7-22" name="__codelineno-7-22" href="#__codelineno-7-22"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_FORCE_UPDATE_DEFAULT_GPU</span><span class="o">=</span><span class="nb">true</span>
</span><span id="__span-7-23"><a id="__codelineno-7-23" name="__codelineno-7-23" href="#__codelineno-7-23"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_ENABLE_DIRECT_GPU_COMM</span><span class="o">=</span><span class="m">1</span>
</span><span id="__span-7-24"><a id="__codelineno-7-24" name="__codelineno-7-24" href="#__codelineno-7-24"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_FORCE_GPU_AWARE_MPI</span><span class="o">=</span><span class="m">1</span>
</span><span id="__span-7-25"><a id="__codelineno-7-25" name="__codelineno-7-25" href="#__codelineno-7-25"></a>
</span><span id="__span-7-26"><a id="__codelineno-7-26" name="__codelineno-7-26" href="#__codelineno-7-26"></a><span class="c1"># Add your input (tpr) file in the command below</span>
</span><span id="__span-7-27"><a id="__codelineno-7-27" name="__codelineno-7-27" href="#__codelineno-7-27"></a>srun<span class="w"> </span>gmx_mpi<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>step6.0_minimization.mdp<span class="w"> </span>-o<span class="w"> </span>step6.0_minimization.tpr<span class="w"> </span>-c<span class="w"> </span>step5_input.gro<span class="w"> </span>-r<span class="w"> </span>step5_input.gro<span class="w"> </span>-p<span class="w"> </span>topol.top<span class="w"> </span>-n<span class="w"> </span>index.ndx
</span><span id="__span-7-28"><a id="__codelineno-7-28" name="__codelineno-7-28" href="#__codelineno-7-28"></a>srun<span class="w"> </span>gmx_mpi<span class="w"> </span>mdrun<span class="w"> </span>-s<span class="w"> </span>step6.0_minimization.tpr<span class="w"> </span>-ntomp<span class="w"> </span><span class="si">${</span><span class="nv">SLURM_CPUS_PER_TASK</span><span class="si">}</span>
</span></code></pre></div>
<h3 id="sbatch-gh-2-gpu-18-omp-threads-2-mpi-ranks">SBATCH GH, 2 GPU, 18 OMP threads, 2 MPI ranks<a class="headerlink" href="#sbatch-gh-2-gpu-18-omp-threads-2-mpi-ranks" title="Permanent link"></a></h3>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-8-1"><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="ch">#!/bin/bash</span>
</span><span id="__span-8-2"><a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="c1">#SBATCH --time=00:10:00 # maximum execution time of 10 minutes</span>
</span><span id="__span-8-3"><a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="c1">#SBATCH --output=_scheduler-stdout.txt</span>
</span><span id="__span-8-4"><a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="c1">#SBATCH --error=_scheduler-stderr.txt</span>
</span><span id="__span-8-5"><a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="c1">#SBATCH --nodes=1 # number of GH200 nodes with each node having 4 CPU+GPU</span>
</span><span id="__span-8-6"><a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a><span class="c1">#SBATCH --ntasks-per-node=2 # 2 MPI ranks per node</span>
</span><span id="__span-8-7"><a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="c1">#SBATCH --cpus-per-task=18 # 18 OMP threads per MPI rank</span>
</span><span id="__span-8-8"><a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a><span class="c1">#SBATCH --cluster=gmerlin7</span>
</span><span id="__span-8-9"><a id="__codelineno-8-9" name="__codelineno-8-9" href="#__codelineno-8-9"></a><span class="c1">#SBATCH --hint=nomultithread</span>
</span><span id="__span-8-10"><a id="__codelineno-8-10" name="__codelineno-8-10" href="#__codelineno-8-10"></a><span class="c1">#SBATCH --partition=gh-hourly</span>
</span><span id="__span-8-11"><a id="__codelineno-8-11" name="__codelineno-8-11" href="#__codelineno-8-11"></a><span class="c1">#SBATCH --gpus=2</span>
</span><span id="__span-8-12"><a id="__codelineno-8-12" name="__codelineno-8-12" href="#__codelineno-8-12"></a>
</span><span id="__span-8-13"><a id="__codelineno-8-13" name="__codelineno-8-13" href="#__codelineno-8-13"></a><span class="nb">unset</span><span class="w"> </span>PMODULES_ENV
</span><span id="__span-8-14"><a id="__codelineno-8-14" name="__codelineno-8-14" href="#__codelineno-8-14"></a>module<span class="w"> </span>purge
</span><span id="__span-8-15"><a id="__codelineno-8-15" name="__codelineno-8-15" href="#__codelineno-8-15"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-8-16"><a id="__codelineno-8-16" name="__codelineno-8-16" href="#__codelineno-8-16"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.7-blxc-GH200-gpu<span class="w"> </span>gromacs/2025.2-cjnq-GH200-gpu-omp
</span><span id="__span-8-17"><a id="__codelineno-8-17" name="__codelineno-8-17" href="#__codelineno-8-17"></a>
</span><span id="__span-8-18"><a id="__codelineno-8-18" name="__codelineno-8-18" href="#__codelineno-8-18"></a><span class="nb">export</span><span class="w"> </span><span class="nv">FI_CXI_RX_MATCH_MODE</span><span class="o">=</span>software
</span><span id="__span-8-19"><a id="__codelineno-8-19" name="__codelineno-8-19" href="#__codelineno-8-19"></a>
</span><span id="__span-8-20"><a id="__codelineno-8-20" name="__codelineno-8-20" href="#__codelineno-8-20"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_GPU_DD_COMMS</span><span class="o">=</span><span class="nb">true</span>
</span><span id="__span-8-21"><a id="__codelineno-8-21" name="__codelineno-8-21" href="#__codelineno-8-21"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_GPU_PME_PP_COMMS</span><span class="o">=</span><span class="nb">true</span>
</span><span id="__span-8-22"><a id="__codelineno-8-22" name="__codelineno-8-22" href="#__codelineno-8-22"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_FORCE_UPDATE_DEFAULT_GPU</span><span class="o">=</span><span class="nb">true</span>
</span><span id="__span-8-23"><a id="__codelineno-8-23" name="__codelineno-8-23" href="#__codelineno-8-23"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_ENABLE_DIRECT_GPU_COMM</span><span class="o">=</span><span class="m">1</span>
</span><span id="__span-8-24"><a id="__codelineno-8-24" name="__codelineno-8-24" href="#__codelineno-8-24"></a><span class="nb">export</span><span class="w"> </span><span class="nv">GMX_FORCE_GPU_AWARE_MPI</span><span class="o">=</span><span class="m">1</span>
</span><span id="__span-8-25"><a id="__codelineno-8-25" name="__codelineno-8-25" href="#__codelineno-8-25"></a>
</span><span id="__span-8-26"><a id="__codelineno-8-26" name="__codelineno-8-26" href="#__codelineno-8-26"></a><span class="c1"># Add your input (tpr) file in the command below</span>
</span><span id="__span-8-27"><a id="__codelineno-8-27" name="__codelineno-8-27" href="#__codelineno-8-27"></a>srun<span class="w"> </span>gmx_mpi<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>step6.0_minimization.mdp<span class="w"> </span>-o<span class="w"> </span>step6.0_minimization.tpr<span class="w"> </span>-c<span class="w"> </span>step5_input.gro<span class="w"> </span>-r<span class="w"> </span>step5_input.gro<span class="w"> </span>-p<span class="w"> </span>topol.top<span class="w"> </span>-n<span class="w"> </span>index.ndx
</span><span id="__span-8-28"><a id="__codelineno-8-28" name="__codelineno-8-28" href="#__codelineno-8-28"></a>srun<span class="w"> </span>gmx_mpi<span class="w"> </span>mdrun<span class="w"> </span>-s<span class="w"> </span>step6.0_minimization.tpr<span class="w"> </span>-ntomp<span class="w"> </span><span class="si">${</span><span class="nv">SLURM_CPUS_PER_TASK</span><span class="si">}</span>
</span></code></pre></div>
<h2 id="developing-your-own-gpu-code">Developing your own GPU code<a class="headerlink" href="#developing-your-own-gpu-code" title="Permanent link"></a></h2>
<h4 id="a100">A100<a class="headerlink" href="#a100" title="Permanent link"></a></h4>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-9-1"><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a>module<span class="w"> </span>purge
</span><span id="__span-9-2"><a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>module<span class="w"> </span>use<span class="w"> </span>Spack<span class="w"> </span>unstable
</span><span id="__span-9-3"><a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>module<span class="w"> </span>load<span class="w"> </span>gcc/12.3<span class="w"> </span>openmpi/5.0.7-3vzj-A100-gpu<span class="w"> </span>gromacs/2025.2-vbj4-A100-gpu-omp<span class="w"> </span>cmake/3.31.6-o3lb<span class="w"> </span>python/3.13.1-cyro
</span><span id="__span-9-4"><a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a>
</span><span id="__span-9-5"><a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/gromacs/gromacs.git
</span><span id="__span-9-6"><a id="__codelineno-9-6" name="__codelineno-9-6" href="#__codelineno-9-6"></a><span class="nb">cd</span><span class="w"> </span>gromacs
</span><span id="__span-9-7"><a id="__codelineno-9-7" name="__codelineno-9-7" href="#__codelineno-9-7"></a>
</span><span id="__span-9-8"><a id="__codelineno-9-8" name="__codelineno-9-8" href="#__codelineno-9-8"></a>mkdir<span class="w"> </span>build<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>build
</span><span id="__span-9-9"><a id="__codelineno-9-9" name="__codelineno-9-9" href="#__codelineno-9-9"></a>cmake<span class="w"> </span>-DCMAKE_C_COMPILER<span class="o">=</span>gcc-12<span class="w"> </span><span class="se">\</span>
</span><span id="__span-9-10"><a id="__codelineno-9-10" name="__codelineno-9-10" href="#__codelineno-9-10"></a><span class="w"> </span>-DCMAKE_CXX_COMPILER<span class="o">=</span>g++-12<span class="w"> </span><span class="se">\</span>
</span><span id="__span-9-11"><a id="__codelineno-9-11" name="__codelineno-9-11" href="#__codelineno-9-11"></a><span class="w"> </span>-DGMX_MPI<span class="o">=</span>on<span class="w"> </span><span class="se">\</span>
</span><span id="__span-9-12"><a id="__codelineno-9-12" name="__codelineno-9-12" href="#__codelineno-9-12"></a><span class="w"> </span>-DGMX_GPU<span class="o">=</span>CUDA<span class="w"> </span><span class="se">\</span>
</span><span id="__span-9-13"><a id="__codelineno-9-13" name="__codelineno-9-13" href="#__codelineno-9-13"></a><span class="w"> </span>-GMX_CUDA_TARGET_SM<span class="o">=</span><span class="s2">"80"</span><span class="w"> </span><span class="se">\ </span><span class="c1"># 90 for the Hopper GPUs</span>
</span><span id="__span-9-14"><a id="__codelineno-9-14" name="__codelineno-9-14" href="#__codelineno-9-14"></a><span class="w"> </span>-DGMX_DOUBLE<span class="o">=</span>off<span class="w"> </span><span class="se">\ </span><span class="c1"># turn on double precision only if useful</span>
</span><span id="__span-9-15"><a id="__codelineno-9-15" name="__codelineno-9-15" href="#__codelineno-9-15"></a><span class="w"> </span>..
</span><span id="__span-9-16"><a id="__codelineno-9-16" name="__codelineno-9-16" href="#__codelineno-9-16"></a>
</span><span id="__span-9-17"><a id="__codelineno-9-17" name="__codelineno-9-17" href="#__codelineno-9-17"></a>make
</span></code></pre></div>
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