RELION 1.1.0

pts/relion-1.1.0 - 19 June 2023 - Update against Relion 4.0.1 upstream.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.8.4-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://github.com/3dem/relion/archive/refs/tags/4.0.1.tar.gz</URL>
      <MD5>8c7b3d8c9da1691b40c9c8d77b481804</MD5>
      <SHA256>0ebbd94ad922d7f457e3f3b81f5660e2691a845d9a53f0f1c9fbeb4e54cd5c17</SHA256>
      <FileName>relion-4.0.1.tar.gz</FileName>
      <FileSize>3345990</FileSize>
    </Package>
    <Package>
      <URL>ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion_benchmark.tar.gz</URL>
      <MD5>5cbb5bfdab75fca6bfe05e7848ccf26c</MD5>
      <SHA256>c7d34a1c98ba956aa0a9b4534921c285c07bab4b9bd8ac3ee1604353c6cccd11</SHA256>
      <FileName>relion_benchmark.tar.gz</FileName>
      <FileSize>50671399402</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/bash
tar -xf relion-4.0.1.tar.gz
cd relion-4.0.1
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release -DGUI=OFF
make -j $NUM_CPU_CORES
retVal=$?
if [ $retVal -ne 0 ]; then
    echo $retVal > ~/install-exit-status
    exit $retVal
fi
cd ~/
tar -xf relion_benchmark.tar.gz
cat>relion<<EOT
#!/bin/sh
cd relion_benchmark/
mpirun --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES ~/relion-4.0.1/build/bin/relion_refine_mpi --i ~/relion_benchmark/Particles/shiny_2sets.star --o out \$@ > \$LOG_FILE 2>&1
echo \$? > ~/test-exit-status
EOT
chmod +x relion

interim.sh

#!/bin/bash
rm -rf relion_benchmark/out
mkdir relion_benchmark/out

post.sh

#!/bin/bash
rm -rf relion_benchmark/out
mkdir relion_benchmark/out

pre.sh

#!/bin/bash
rm -rf relion_benchmark/out
mkdir relion_benchmark/out

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.8.4-->
<PhoronixTestSuite>
  <SystemMonitor>
    <Sensor>sys.time</Sensor>
  </SystemMonitor>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.8.4-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>RELION</Title>
    <AppVersion>4.0.1</AppVersion>
    <Description>RELION - REgularised LIkelihood OptimisatioN - is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy (cryo-EM). It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology.</Description>
    <ResultScale>Seconds</ResultScale>
    <Proportion>LIB</Proportion>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.1.0</Version>
    <SupportedPlatforms>Linux</SupportedPlatforms>
    <SoftwareType>Scientific</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>openmpi-development, fftw3-development, git, cmake, tiff, build-utilities</ExternalDependencies>
    <EnvironmentSize>56000</EnvironmentSize>
    <ProjectURL>https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page</ProjectURL>
    <RepositoryURL>https://github.com/3dem/relion</RepositoryURL>
    <Maintainer>Michael Larabel</Maintainer>
  </TestProfile>
  <TestSettings>
    <Option>
      <DisplayName>Test</DisplayName>
      <Identifier>test</Identifier>
      <Menu>
        <Entry>
          <Name>Basic</Name>
          <Value>--iter 1</Value>
          <Message>Run on modern desktops in ~30 minutes.</Message>
        </Entry>
        <Entry>
          <Name>Class2D</Name>
          <Value>--ctf --iter 1 --tau2_fudge 2 --particle_diameter 360 --K 200 --zero_mask --oversampling 1 --psi_step 6 --offset_range 5 --offset_step 2 --norm --scale --random_seed 0</Value>
          <Message>Very time consuming unless on huge core count systems.</Message>
        </Entry>
        <Entry>
          <Name>Class3D</Name>
          <Value>--ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 1 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0</Value>
          <Message>Very time consuming unless on huge core count systems.</Message>
        </Entry>
      </Menu>
    </Option>
    <Option>
      <DisplayName>Device</DisplayName>
      <Identifier>device</Identifier>
      <Menu>
        <Entry>
          <Name>CPU</Name>
          <Value>--cpu --j 1</Value>
        </Entry>
      </Menu>
    </Option>
  </TestSettings>
</PhoronixTestSuite>