Timed HMMer Search 1.3.0

pts/hmmer-1.3.0 - 05 May 2021 - Update against HMMER 3.3.2 upstream, switch to MPI version rather than the threads.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.4.0m1-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz</URL>
      <MD5>ea03d88b4e8228a1dc6d84d56af27195</MD5>
      <SHA256>92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69</SHA256>
      <FileName>hmmer-3.3.2.tar.gz</FileName>
      <FileSize>18213049</FileSize>
    </Package>
    <Package>
      <URL>http://www.phoronix-test-suite.com/benchmark-files/Pfam_ls.gz</URL>
      <MD5>bcc3ea17f61eb22dc0d4375f79e0ced5</MD5>
      <SHA256>8cee7f076530c743042e32fdbf32b816af4459f1ebf1cb39586928018c918c52</SHA256>
      <FileName>Pfam_ls.gz</FileName>
      <FileSize>83797216</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

tar -zxvf hmmer-3.3.2.tar.gz
cd hmmer-3.3.2/
./configure --enable-mpi
if [ $OS_TYPE = "BSD" ]
then
	gmake -j $NUM_CPU_CORES
else
	make -j $NUM_CPU_CORES
fi
echo $? > ~/install-exit-status
cd ~
gunzip Pfam_ls.gz -c > hmmer-3.3.2/tutorial/Pfam_ls

cat>hmmer<<EOT
#!/bin/sh
cd hmmer-3.3.2/tutorial
 mpirun --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES ../src/hmmsearch Pfam_ls 7LESS_DROME
echo \$? > ~/test-exit-status
EOT
chmod +x hmmer

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.4.0m1-->
<PhoronixTestSuite>
  <SystemMonitor>
    <Sensor>sys.time</Sensor>
  </SystemMonitor>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.4.0m1-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>Timed HMMer Search</Title>
    <AppVersion>3.3.2</AppVersion>
    <Description>This test searches through the Pfam database of profile hidden markov models. The search finds the domain structure of Drosophila Sevenless protein.</Description>
    <ResultScale>Seconds</ResultScale>
    <Proportion>LIB</Proportion>
    <SubTitle>Pfam Database Search</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.3.0</Version>
    <SupportedPlatforms>Linux, Solaris, BSD, MacOSX</SupportedPlatforms>
    <SoftwareType>Scientific</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>build-utilities, openmpi-development</ExternalDependencies>
    <EnvironmentSize>719</EnvironmentSize>
    <ProjectURL>http://hmmer.org/</ProjectURL>
    <InternalTags>SMP</InternalTags>
    <Maintainer>Andrew Schofield</Maintainer>
  </TestProfile>
</PhoronixTestSuite>