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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>