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Merge pull request #1125 from virtualcell/test_ci
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Test ci
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@jcschaff
jcschaff committed Feb 2, 2024
2 parents 578ac79 + 9730f97 commit 7fb69ed
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Showing 2 changed files with 95 additions and 88 deletions.
10 changes: 8 additions & 2 deletions vcell-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -657,7 +657,6 @@
</goals>
<configuration>
<url>https://github.com/virtualcell/vcell-solvers/releases/download/v0.0.44-dev2/linux64.tgz</url>
<unpack>true</unpack>
<outputDirectory>${project.build.directory}/../../localsolvers/linux64</outputDirectory>
</configuration>
</execution>
Expand Down Expand Up @@ -741,14 +740,21 @@
</configuration>
</execution>
<execution>
<id>chmod-langevin-linux64</id>
<id>process-solvers-linux64</id>
<phase>process-test-resources</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<target>
<chmod file="${project.build.directory}/../../localsolvers/linux64/langevin_x64" perm="755"/>
<exec executable="tar">
<arg value="xzfh"/>
<arg value="${project.build.directory}/../../localsolvers/linux64/linux64.tgz"/>
<arg value="-C"/>
<arg value="${project.build.directory}/../../localsolvers/linux64"/>
</exec>
<delete file="${project.build.directory}/../../localsolvers/linux64/linux64.tgz"/>
</target>
</configuration>
</execution>
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173 changes: 87 additions & 86 deletions vcell-core/src/main/java/cbit/vcell/solvers/AbstractCompiledSolver.java
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Original file line number Diff line number Diff line change
Expand Up @@ -197,92 +197,93 @@ public void runSolver() {

private void checkLinuxSharedLibs() throws IOException, InterruptedException {
if (OperatingSystemInfo.getInstance().isLinux()) {
File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
File mySolverLinkDir = new File(localSimDir, simTask.getSimKey().toString() + ResourceUtil.LOCAL_SOLVER_LIB_LINK_SUFFIX);
if (mySolverLinkDir.exists()) {
File[] temp = mySolverLinkDir.listFiles();
for (int i = 0; i < temp.length; i++) {
temp[i].delete();
}
} else {
mySolverLinkDir.mkdir();
}
SolverDescription mySolverDescription = getSimulationJob().getSimulation().getSolverTaskDescription().getSolverDescription();
File localSolverPath = SolverUtilities.getExes(mySolverDescription)[0];
Path linkSolver = createSymbolicLink(mySolverLinkDir, localSolverPath.getName(), localSolverPath);
final String LD_LIB_PATH = "LD_LIBRARY_PATH";
String newLD_LIB_PATH = mySolverLinkDir.getAbsolutePath();
File solversDir = ResourceUtil.getLocalSolversDirectory();
// System.out.println("-----reading solverdir libs "+solversDir.getAbsolutePath());
ArrayList<File> tempAL = new ArrayList<File>();
File[] temp = solversDir.listFiles();
for (int i = 0; i < temp.length; i++) {
if (temp[i].getName().startsWith("lib") && temp[i].isFile() && temp[i].length() != 0 && !Files.isSymbolicLink(temp[i].toPath())) {
tempAL.add(temp[i]);
// System.out.println(temp[i].getName());
}
}
File[] libzipSolverFiles = (File[]) tempAL.toArray(new File[0]);
ProcessBuilder pb = new ProcessBuilder("ldd", linkSolver.toString());
pb.redirectErrorStream(true);
Process p = pb.start();
int ioByte = -1;
StringBuffer sb = new StringBuffer();
while ((ioByte = p.getInputStream().read()) != -1) {
sb.append((char) ioByte);
}
p.waitFor();
// System.out.println("-----ldd output:\n"+sb.toString());

//Try to save output to file for cli without interfering with further processing
File stdOutFile = new File(String.valueOf(Paths.get(System.getProperty("user.dir"))), "stdOut.txt");
try (BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(stdOutFile))){
bos.write(sb.toString().getBytes());
}catch(Exception e) {
lg.error(e.getMessage(), e);
}

java.io.BufferedReader br = new java.io.BufferedReader(new java.io.StringReader(sb.toString()));
String line = null;
// System.out.println("-----reading ldd:");
while ((line = br.readLine()) != null) {
// System.out.println(line);
java.util.StringTokenizer libInfo = new java.util.StringTokenizer(line, " \t");
if (libInfo.countTokens() == 4) {// "libname => libpath offset" -or- "libname => not found"
String libName = libInfo.nextToken();
String ptr = libInfo.nextToken();
String libPath = libInfo.nextToken();
String aux = libInfo.nextToken();
if (libPath.equals("not") && aux.equals("found")) {
boolean bMatch = false;
for (int i = 0; i < libzipSolverFiles.length; i++) {
if (libzipSolverFiles[i].getName().startsWith(libName) && libzipSolverFiles[i].length() != 0) {
//System.out.println(libName+" "+ptr+" "+libPath+" "+aux+" "+org.apache.commons.lang3.StringUtils.getJaroWinklerDistance("libhdf5.so",libName));
// System.out.println(libName+" "+ptr+" "+libPath+" "+aux+" match="+libzipSolverFiles[i]);
createSymbolicLink(mySolverLinkDir, libName, libzipSolverFiles[i]);
bMatch = true;
break;
}
}
if (!bMatch) {
for (int i = 0; i < libzipSolverFiles.length; i++) {
int index = libName.indexOf(".so");
if (index != -1) {
String matchName = libName.substring(0, index + 3);
if (libzipSolverFiles[i].getName().startsWith(matchName) && libzipSolverFiles[i].length() != 0) {
// System.out.println("ALTERNATE "+libName+" "+ptr+" "+libPath+" "+aux+" match="+libzipSolverFiles[i]);
createSymbolicLink(mySolverLinkDir, libName, libzipSolverFiles[i]);
break;
}
}
}
}
}
}
}

// System.out.println("-----Setting executable "+LD_LIB_PATH+" to "+newLD_LIB_PATH);
getMathExecutable().addEnvironmentVariable(LD_LIB_PATH, newLD_LIB_PATH);
// File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
// File mySolverLinkDir = new File(localSimDir, simTask.getSimKey().toString() + ResourceUtil.LOCAL_SOLVER_LIB_LINK_SUFFIX);
// if (mySolverLinkDir.exists()) {
// File[] temp = mySolverLinkDir.listFiles();
// for (int i = 0; i < temp.length; i++) {
// temp[i].delete();
// }
// } else {
// mySolverLinkDir.mkdir();
// }
// SolverDescription mySolverDescription = getSimulationJob().getSimulation().getSolverTaskDescription().getSolverDescription();
// File localSolverPath = SolverUtilities.getExes(mySolverDescription)[0];
// Path linkSolver = createSymbolicLink(mySolverLinkDir, localSolverPath.getName(), localSolverPath);
// final String LD_LIB_PATH = "LD_LIBRARY_PATH";
// String newLD_LIB_PATH = mySolverLinkDir.getAbsolutePath();
// File solversDir = ResourceUtil.getLocalSolversDirectory();
//// System.out.println("-----reading solverdir libs "+solversDir.getAbsolutePath());
// ArrayList<File> tempAL = new ArrayList<File>();
// File[] temp = solversDir.listFiles();
// for (int i = 0; i < temp.length; i++) {
// if (temp[i].getName().startsWith("lib") && temp[i].isFile() && temp[i].length() != 0 && !Files.isSymbolicLink(temp[i].toPath())) {
// tempAL.add(temp[i]);
//// System.out.println(temp[i].getName());
// }
// }
// File[] libzipSolverFiles = (File[]) tempAL.toArray(new File[0]);
// ProcessBuilder pb = new ProcessBuilder("ldd", linkSolver.toString());
// pb.redirectErrorStream(true);
// Process p = pb.start();
// int ioByte = -1;
// StringBuffer sb = new StringBuffer();
// while ((ioByte = p.getInputStream().read()) != -1) {
// sb.append((char) ioByte);
// }
// p.waitFor();
//// System.out.println("-----ldd output:\n"+sb.toString());
//
// //Try to save output to file for cli without interfering with further processing
// File stdOutFile = new File(String.valueOf(Paths.get(System.getProperty("user.dir"))), "stdOut.txt");
// try (BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(stdOutFile))){
// bos.write(sb.toString().getBytes());
// }catch(Exception e) {
// lg.error(e.getMessage(), e);
// }
//
// java.io.BufferedReader br = new java.io.BufferedReader(new java.io.StringReader(sb.toString()));
// String line = null;
//// System.out.println("-----reading ldd:");
// while ((line = br.readLine()) != null) {
//// System.out.println(line);
// java.util.StringTokenizer libInfo = new java.util.StringTokenizer(line, " \t");
// if (libInfo.countTokens() == 4) {// "libname => libpath offset" -or- "libname => not found"
// String libName = libInfo.nextToken();
// String ptr = libInfo.nextToken();
// String libPath = libInfo.nextToken();
// String aux = libInfo.nextToken();
// if (libPath.equals("not") && aux.equals("found")) {
// boolean bMatch = false;
// for (int i = 0; i < libzipSolverFiles.length; i++) {
// if (libzipSolverFiles[i].getName().startsWith(libName) && libzipSolverFiles[i].length() != 0) {
// //System.out.println(libName+" "+ptr+" "+libPath+" "+aux+" "+org.apache.commons.lang3.StringUtils.getJaroWinklerDistance("libhdf5.so",libName));
//// System.out.println(libName+" "+ptr+" "+libPath+" "+aux+" match="+libzipSolverFiles[i]);
// createSymbolicLink(mySolverLinkDir, libName, libzipSolverFiles[i]);
// bMatch = true;
// break;
// }
// }
// if (!bMatch) {
// for (int i = 0; i < libzipSolverFiles.length; i++) {
// int index = libName.indexOf(".so");
// if (index != -1) {
// String matchName = libName.substring(0, index + 3);
// if (libzipSolverFiles[i].getName().startsWith(matchName) && libzipSolverFiles[i].length() != 0) {
//// System.out.println("ALTERNATE "+libName+" "+ptr+" "+libPath+" "+aux+" match="+libzipSolverFiles[i]);
// createSymbolicLink(mySolverLinkDir, libName, libzipSolverFiles[i]);
// break;
// }
// }
// }
// }
// }
// }
// }
//
//// System.out.println("-----Setting executable "+LD_LIB_PATH+" to "+newLD_LIB_PATH);
// getMathExecutable().addEnvironmentVariable(LD_LIB_PATH, newLD_LIB_PATH);
getMathExecutable().addEnvironmentVariable("LD_LIBRARY_PATH", ResourceUtil.getLocalSolversDirectory().getCanonicalPath());
}else if (OperatingSystemInfo.getInstance().isMac()) {
getMathExecutable().addEnvironmentVariable("HDF5_DISABLE_VERSION_CHECK", "1");
}
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