Repository: airavata Updated Branches: refs/heads/master f5693907c -> 03ecceab1
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a22a355/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt b/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt index e749e9c..cf8dfb6 100644 --- a/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt +++ b/modules/gfac/gfac-ssh/src/test/resources/PBSTemplate.xslt @@ -5,11 +5,11 @@ in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY ~ KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. --> -<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"; xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12";> +<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"; xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12";> <xsl:output method="text" /> <xsl:template match="/ns:JobDescriptor"> #! /bin/sh -# PBS batch job script built by Globus job manager +# PBS batch job submission script generated by Apache Airavata # <xsl:choose> <xsl:when test="ns:shellName"> ##PBS -S <xsl:value-of select="ns:shellName"/> @@ -59,8 +59,10 @@ export<xsl:text> </xsl:text><xsl:value-of select="."/> <xsl:value-of select="."/><xsl:text> </xsl:text> </xsl:for-each> cd <xsl:text> </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>
</xsl:text> - <xsl:choose><xsl:when test="ns:jobSubmitterCommand"> -<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text> </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text> </xsl:text> + <xsl:choose><xsl:when test="ns:jobSubmitterCommand != ''"> +<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text> </xsl:text> +<xsl:value-of select="ns:cpuCount"/><xsl:text> </xsl:text> + </xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text> </xsl:text> <xsl:for-each select="ns:inputs/ns:input"> <xsl:value-of select="."/><xsl:text> </xsl:text> </xsl:for-each> http://git-wip-us.apache.org/repos/asf/airavata/blob/5a22a355/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java index f7516c7..23c0122 100644 --- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java +++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/PBSOutputParser.java @@ -158,25 +158,25 @@ public class PBSOutputParser implements OutputParser { public void parse(String userName, Map<String, JobStatus> statusMap, String rawOutput) { log.debug(rawOutput); - String[] info = rawOutput.split("\n"); + String[] info = rawOutput.split("\n"); int lastStop = 0; for (String jobID : statusMap.keySet()) { - for(int i=lastStop;i<info.length;i++){ - if(jobID.contains(info[i].split(" ")[0]) && !"".equals(info[i].split(" ")[0])){ - // now starts processing this line - log.info(info[i]); - String correctLine = info[i]; - String[] columns = correctLine.split(" "); - List<String> columnList = new ArrayList<String>(); - for (String s : columns) { - if (!"".equals(s)) { - columnList.add(s); - } - } - lastStop = i+1; - statusMap.put(jobID, JobStatus.valueOf(columnList.get(9))); - break; - } + for (int i = lastStop; i < info.length; i++) { + if (jobID.split(",")[0].contains(info[i].split(" ")[0]) && !"".equals(info[i].split(" ")[0])) { + // now starts processing this line + log.info(info[i]); + String correctLine = info[i]; + String[] columns = correctLine.split(" "); + List<String> columnList = new ArrayList<String>(); + for (String s : columns) { + if (!"".equals(s)) { + columnList.add(s); + } + } + lastStop = i + 1; + statusMap.put(jobID, JobStatus.valueOf(columnList.get(9))); + break; + } } } } http://git-wip-us.apache.org/repos/asf/airavata/blob/5a22a355/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java index b2c0cff..ab60bb3 100644 --- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java +++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SGEOutputParser.java @@ -135,7 +135,7 @@ public class SGEOutputParser implements OutputParser{ int lastStop = 0; for (String jobID : statusMap.keySet()) { for(int i=lastStop;i<info.length;i++){ - if(jobID.contains(info[i].split(" ")[0]) && !"".equals(info[i].split(" ")[0])){ + if(jobID.split(",")[0].contains(info[i].split(" ")[0]) && !"".equals(info[i].split(" ")[0])){ // now starts processing this line log.info(info[i]); String correctLine = info[i]; http://git-wip-us.apache.org/repos/asf/airavata/blob/5a22a355/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java index 5738dd9..717caae 100644 --- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java +++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/SlurmOutputParser.java @@ -34,7 +34,7 @@ public class SlurmOutputParser implements OutputParser { private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class); public void parse(JobDescriptor descriptor, String rawOutput)throws SSHApiException { - log.debug(rawOutput); + log.info(rawOutput); String[] info = rawOutput.split("\n"); String lastString = info[info.length -1]; if (lastString.contains("JOB ID")) { @@ -94,7 +94,7 @@ public class SlurmOutputParser implements OutputParser { * @return */ public String parse(String rawOutput) throws SSHApiException { - log.debug(rawOutput); + log.info(rawOutput); String[] info = rawOutput.split("\n"); for (String anInfo : info) { if (anInfo.contains("Submitted batch job")) { @@ -102,11 +102,12 @@ public class SlurmOutputParser implements OutputParser { return split[1].trim(); } } - throw new SSHApiException(rawOutput); //To change body of implemented methods use File | Settings | File Templates. + return ""; +// throw new SSHApiException(rawOutput); //todo//To change body of implemented methods use File | Settings | File Templates. } public JobStatus parse(String jobID, String rawOutput)throws SSHApiException { - log.debug(rawOutput); + log.info(rawOutput); String[] info = rawOutput.split("\n"); String lastString = info[info.length -1]; if (lastString.contains("JOBID") || lastString.contains("PARTITION")) { @@ -148,7 +149,7 @@ public class SlurmOutputParser implements OutputParser { } public void parse(String userName, Map<String, JobStatus> statusMap, String rawOutput) throws SSHApiException { - log.debug(rawOutput); + log.info(rawOutput); String[] info = rawOutput.split("\n"); String lastString = info[info.length -1]; if (lastString.contains("JOBID") || lastString.contains("PARTITION")) { @@ -157,22 +158,24 @@ public class SlurmOutputParser implements OutputParser { } int lastStop = 0; for (String jobID : statusMap.keySet()) { - for(int i=lastStop;i<info.length;i++){ - if(info[i].contains(jobID)){ - // now starts processing this line - log.info(info[i]); - String correctLine = info[i]; - String[] columns = correctLine.split(" "); - List<String> columnList = new ArrayList<String>(); - for (String s : columns) { - if (!"".equals(s)) { - columnList.add(s); - } - } - lastStop = i+1; - statusMap.put(jobID, JobStatus.valueOf(columnList.get(4))); - break; - } + String jobId = jobID.split(",")[0]; + String jobName = jobID.split(",")[1]; + for (int i = lastStop; i < info.length; i++) { + if (info[i].contains(jobId) || info[i].contains(jobName.substring(0,8))) { + // now starts processing this line + log.info(info[i]); + String correctLine = info[i]; + String[] columns = correctLine.split(" "); + List<String> columnList = new ArrayList<String>(); + for (String s : columns) { + if (!"".equals(s)) { + columnList.add(s); + } + } + lastStop = i + 1; + statusMap.put(jobID, JobStatus.valueOf(columnList.get(4))); + break; + } } } }
