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Posted to commits@airavata.apache.org by sh...@apache.org on 2014/11/14 21:24:54 UTC
[1/2] airavata git commit: Added create experiment methods for
gromacs, expressos, lammps, nwchem, trinity, and autodock on stampede
Repository: airavata
Updated Branches:
refs/heads/master 2330ad894 -> d3aff435e
Added create experiment methods for gromacs, expressos, lammps, nwchem, trinity, and autodock on stampede
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/3eacfb88
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/3eacfb88
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/3eacfb88
Branch: refs/heads/master
Commit: 3eacfb884f61457b3b64b44cfeae9d79abc54065
Parents: c8bf7f1
Author: shamrath <sh...@gmail.com>
Authored: Fri Nov 14 15:24:25 2014 -0500
Committer: shamrath <sh...@gmail.com>
Committed: Fri Nov 14 15:24:25 2014 -0500
----------------------------------------------------------------------
.../client/samples/CreateLaunchExperiment.java | 581 +++++++++++++++++--
1 file changed, 543 insertions(+), 38 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/3eacfb88/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
index d281dc9..34d419c 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
@@ -45,7 +45,6 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
-import java.util.Random;
import java.util.UUID;
public class CreateLaunchExperiment {
@@ -59,8 +58,15 @@ public class CreateLaunchExperiment {
private static Airavata.Client airavataClient;
private static String echoAppId = "Echo_36fbb479-5b41-4f48-a9c5-382ee910ac6b";
- private static String wrfAppId = "WRF_a37fb0be-a252-4185-a31c-ff43f585f88f";
- private static String amberAppId = "Amber_a8187edf-7be0-4dad-9c8a-d0cc9075e6a0";
+ private static String wrfAppId = "WRF_7ad5da38-c08b-417c-a9ea-da9298839762";
+ private static String amberAppId = "Amber_49b16f6f-93ab-4885-9971-6ab2ab5eb3d3";
+ private static String gromacsAppId = "GROMACS_05622038-9edd-4cb1-824e-0b7cb993364b";
+ private static String espressoAppId = "ESPRESSO_10cc2820-5d0b-4c63-9546-8a8b595593c1";
+ private static String lammpsAppId = "LAMMPS_10893eb5-3840-438c-8446-d26c7ecb001f";
+ private static String nwchemAppId = "NWChem_2c8fee64-acf9-4a89-b6d3-91eb53c7640c";
+ private static String trinityAppId = "Trinity_e894acf5-9bca-46e8-a1bd-7e2d5155191a";
+ private static String autodockAppId = "AutoDock_43d9fdd0-c404-49f4-b913-3abf9080a8c9";
+
private static String localHost = "localhost";
private static String trestlesHostName = "trestles.sdsc.xsede.org";
@@ -80,35 +86,39 @@ public class CreateLaunchExperiment {
}
private static String fsdResourceId;
-
-
-
+
+
public static void createAndLaunchExp() throws TException {
-// final String expId = createEchoExperimentForFSD(airavataClient);
- try {
- for (int i = 0; i < 1; i++) {
-// final String expId = createExperimentForSSHHost(airavata);
-// final String expId = createEchoExperimentForFSD(airavataClient);
-// final String expId = createEchoExperimentForStampede(airavataClient);
-// final String expId = createEchoExperimentForTrestles(airavataClient);
-// final String expId = createExperimentEchoForLocalHost(airavataClient);
-// final String expId = createExperimentWRFTrestles(airavataClient);
- final String expId = createExperimentForBR2(airavataClient);
-// final String expId = createExperimentForBR2Amber(airavataClient);
-// final String expId = createExperimentWRFStampede(airavataClient);
-// final String expId = createExperimentForStampedeAmber(airavataClient);
-// final String expId = createExperimentForTrestlesAmber(airavataClient);
-
- System.out.println("Experiment ID : " + expId);
-// updateExperiment(airavata, expId);
- launchExperiment(airavataClient, expId);
- }
- } catch (Exception e) {
- logger.error("Error while connecting with server", e.getMessage());
- e.printStackTrace();
+// final String expId = createEchoExperimentForFSD(airavataClient);
+ try {
+ for (int i = 0; i < 1; i++) {
+// final String expId = createExperimentForSSHHost(airavata);
+// final String expId = createEchoExperimentForFSD(airavataClient);
+// final String expId = createEchoExperimentForStampede(airavataClient);
+ final String expId = createEchoExperimentForTrestles(airavataClient);
+// final String expId = createExperimentEchoForLocalHost(airavataClient);
+// final String expId = createExperimentWRFTrestles(airavataClient);
+// final String expId = createExperimentForBR2(airavataClient);
+// final String expId = createExperimentForBR2Amber(airavataClient);
+// final String expId = createExperimentWRFStampede(airavataClient);
+// final String expId = createExperimentForStampedeAmber(airavataClient);
+// final String expId = createExperimentForTrestlesAmber(airavataClient);
+// final String expId = createExperimentGROMACSStampede(airavataClient);
+// final String expId = createExperimentESPRESSOStampede(airavataClient);
+// final String expId = createExperimentLAMMPSStampede(airavataClient);
+// final String expId = createExperimentNWCHEMStampede(airavataClient);
+// final String expId = createExperimentTRINITYStampede(airavataClient);
+// final String expId = createExperimentAUTODOCKStampede(airavataClient); // this is not working , we need to register AutoDock app on stampede
+ System.out.println("Experiment ID : " + expId);
+// updateExperiment(airavata, expId);
+ launchExperiment(airavataClient, expId);
+ }
+ } catch (Exception e) {
+ logger.error("Error while connecting with server", e.getMessage());
+ e.printStackTrace();
+ }
}
- }
@@ -281,17 +291,17 @@ public class CreateLaunchExperiment {
InputDataObjectType input = new InputDataObjectType();
input.setName("Config_Namelist_File");
input.setType(DataType.URI);
- input.setValue("/Users/lahirugunathilake/Downloads/wrf_sample_inputs/namelist.input");
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/namelist.input");
InputDataObjectType input1 = new InputDataObjectType();
input1.setName("WRF_Initial_Conditions");
input1.setType(DataType.URI);
- input1.setValue("/Users/lahirugunathilake/Downloads/wrf_sample_inputs/wrfinput_d01");
+ input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfinput_d01");
InputDataObjectType input2 = new InputDataObjectType();
input2.setName("WRF_Boundary_File");
input2.setType(DataType.URI);
- input2.setValue("/Users/lahirugunathilake/Downloads/wrf_sample_inputs/wrfbdy_d01");
+ input2.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfbdy_d01");
exInputs.add(input);
exInputs.add(input1);
@@ -349,23 +359,518 @@ public class CreateLaunchExperiment {
return null;
}
+
+ public static String createExperimentGROMACSStampede(Airavata.Client client) throws TException {
+ try {
+ List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
+ InputDataObjectType input = new InputDataObjectType();
+ input.setName("GROMOS_Coordinate_File");
+ input.setType(DataType.URI);
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/GROMMACS_FILES/pdb1y6l-EM-vacuum.gro");
+
+ InputDataObjectType input1 = new InputDataObjectType();
+ input1.setName("Portable_Input_Binary_File");
+ input1.setType(DataType.URI);
+ input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/GROMMACS_FILES/pdb1y6l-EM-vacuum.tpr");
+
+ exInputs.add(input);
+ exInputs.add(input1);
+
+
+ List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
+ OutputDataObjectType output = new OutputDataObjectType();
+ output.setName("pdb1y6l-EM-vacuum.tpr.trr");
+ output.setType(DataType.URI);
+ output.setValue("");
+
+ OutputDataObjectType output1 = new OutputDataObjectType();
+ output1.setName("pdb1y6l-EM-vacuum.tpr.edr");
+ output1.setType(DataType.URI);
+ output1.setValue("");
+
+ OutputDataObjectType output2 = new OutputDataObjectType();
+ output2.setName("pdb1y6l-EM-vacuum.tpr.log");
+ output2.setType(DataType.URI);
+ output2.setValue("");
+
+ OutputDataObjectType output3 = new OutputDataObjectType();
+ output3.setName("pdb1y6l-EM-vacuum.gro");
+ output3.setType(DataType.URI);
+ output3.setValue("");
+
+ OutputDataObjectType output4 = new OutputDataObjectType();
+ output4.setName("GROMACS.oJobID");
+ output4.setType(DataType.URI);
+ output4.setValue("");
+
+
+ exOut.add(output);
+ exOut.add(output1);
+ exOut.add(output2);
+ exOut.add(output3);
+ exOut.add(output4);
+
+
+ Experiment simpleExperiment =
+ ExperimentModelUtil.createSimpleExperiment("default", "admin", "GromacsExperiment", "Testing", gromacsAppId, exInputs);
+ simpleExperiment.setExperimentOutputs(exOut);
+
+ Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(gromacsAppId);
+ if (computeResources != null && computeResources.size() != 0) {
+ for (String id : computeResources.keySet()) {
+ String resourceName = computeResources.get(id);
+ if (resourceName.equals(stampedeHostName)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ return client.createExperiment(simpleExperiment);
+ }
+ }
+ }
+ } catch (AiravataSystemException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataSystemException(e);
+ } catch (InvalidRequestException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new InvalidRequestException(e);
+ } catch (AiravataClientException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataClientException(e);
+ } catch (TException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new TException(e);
+ }
+ return null;
+ }
+
+ public static String createExperimentESPRESSOStampede(Airavata.Client client) throws TException {
+ try {
+ List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
+ InputDataObjectType input = new InputDataObjectType();
+ input.setName("AI_Pseudopotential_File");
+ input.setType(DataType.URI);
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/ESPRESSO_FILES/Al.sample.in");
+
+ InputDataObjectType input1 = new InputDataObjectType();
+ input1.setName("AI_Primitive_Cell");
+ input1.setType(DataType.URI);
+ input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/ESPRESSO_FILES/Al.pz-vbc.UPF");
+
+ exInputs.add(input);
+ exInputs.add(input1);
+
+
+ List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
+ OutputDataObjectType output = new OutputDataObjectType();
+ output.setName("ESPRESSO_Execution_Log");
+ output.setType(DataType.URI);
+ output.setValue("");
+
+ OutputDataObjectType output1 = new OutputDataObjectType();
+ output1.setName("ESPRESSO_WFC_Binary_file");
+ output1.setType(DataType.URI);
+ output1.setValue("");
+
+ OutputDataObjectType output2 = new OutputDataObjectType();
+ output2.setName("Al_exc3.wfc1");
+ output2.setType(DataType.URI);
+ output2.setValue("");
+
+ OutputDataObjectType output3 = new OutputDataObjectType();
+ output3.setName("Al_exc3.wfc2");
+ output3.setType(DataType.URI);
+ output3.setValue("");
+
+ OutputDataObjectType output4 = new OutputDataObjectType();
+ output4.setName("Al_exc3.wfc3");
+ output4.setType(DataType.URI);
+ output4.setValue("");
+
+ OutputDataObjectType output5 = new OutputDataObjectType();
+ output5.setName("Al_exc3.wfc4");
+ output5.setType(DataType.URI);
+ output5.setValue("");
+
+ OutputDataObjectType output6 = new OutputDataObjectType();
+ output6.setName("ESPRESSO.oJobID");
+ output6.setType(DataType.URI);
+ output6.setValue("");
+
+
+ exOut.add(output);
+ exOut.add(output1);
+ exOut.add(output2);
+ exOut.add(output3);
+ exOut.add(output4);
+ exOut.add(output5);
+ exOut.add(output6);
+
+
+ Experiment simpleExperiment =
+ ExperimentModelUtil.createSimpleExperiment("default", "admin", "EspressoExperiment", "Testing", espressoAppId, exInputs);
+ simpleExperiment.setExperimentOutputs(exOut);
+
+ Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(espressoAppId);
+ if (computeResources != null && computeResources.size() != 0) {
+ for (String id : computeResources.keySet()) {
+ String resourceName = computeResources.get(id);
+ if (resourceName.equals(stampedeHostName)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ return client.createExperiment(simpleExperiment);
+ }
+ }
+ }
+ } catch (AiravataSystemException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataSystemException(e);
+ } catch (InvalidRequestException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new InvalidRequestException(e);
+ } catch (AiravataClientException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataClientException(e);
+ } catch (TException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new TException(e);
+ }
+ return null;
+ }
+
+ public static String createExperimentTRINITYStampede(Airavata.Client client) throws TException {
+ try {
+ List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
+ InputDataObjectType input = new InputDataObjectType();
+ input.setName("RNA_Seq_Left_Input");
+ input.setType(DataType.URI);
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/TRINITY_FILES/reads.left.fq");
+
+ InputDataObjectType input1 = new InputDataObjectType();
+ input1.setName("RNA_Seq_Right_Input");
+ input1.setType(DataType.URI);
+ input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/TRINITY_FILES/reads.right.fq");
+
+ exInputs.add(input);
+ exInputs.add(input1);
+
+
+ List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
+ OutputDataObjectType output = new OutputDataObjectType();
+ output.setName("Trinity_Execution_Log");
+ output.setType(DataType.URI);
+ output.setValue("");
+
+ OutputDataObjectType output1 = new OutputDataObjectType();
+ output1.setName("Trinity_FASTA_File");
+ output1.setType(DataType.URI);
+ output1.setValue("");
+
+ OutputDataObjectType output2 = new OutputDataObjectType();
+ output2.setName("Trinity.oJobID");
+ output2.setType(DataType.URI);
+ output2.setValue("");
+
+
+ exOut.add(output);
+ exOut.add(output1);
+ exOut.add(output2);
+
+ Experiment simpleExperiment =
+ ExperimentModelUtil.createSimpleExperiment("default", "admin", "TrinityExperiment", "Testing", trinityAppId, exInputs);
+ simpleExperiment.setExperimentOutputs(exOut);
+
+ Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(trinityAppId);
+ if (computeResources != null && computeResources.size() != 0) {
+ for (String id : computeResources.keySet()) {
+ String resourceName = computeResources.get(id);
+ if (resourceName.equals(stampedeHostName)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ return client.createExperiment(simpleExperiment);
+ }
+ }
+ }
+ } catch (AiravataSystemException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataSystemException(e);
+ } catch (InvalidRequestException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new InvalidRequestException(e);
+ } catch (AiravataClientException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataClientException(e);
+ } catch (TException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new TException(e);
+ }
+ return null;
+ }
+
+ public static String createExperimentLAMMPSStampede(Airavata.Client client) throws TException {
+ try {
+ List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
+ InputDataObjectType input = new InputDataObjectType();
+ input.setName("Friction_Simulation_Input");
+ input.setType(DataType.URI);
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/LAMMPS_FILES/in.friction");
+
+ exInputs.add(input);
+
+ List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
+ OutputDataObjectType output = new OutputDataObjectType();
+ output.setName("LAMMPS_Simulation_Log");
+ output.setType(DataType.URI);
+ output.setValue("");
+
+ OutputDataObjectType output1 = new OutputDataObjectType();
+ output1.setName("LAMMPS.oJobID");
+ output1.setType(DataType.URI);
+ output1.setValue("");
+
+ exOut.add(output);
+ exOut.add(output1);
+
+ Experiment simpleExperiment =
+ ExperimentModelUtil.createSimpleExperiment("default", "admin", "LAMMPSExperiment", "Testing", lammpsAppId, exInputs);
+ simpleExperiment.setExperimentOutputs(exOut);
+
+ Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(lammpsAppId);
+ if (computeResources != null && computeResources.size() != 0) {
+ for (String id : computeResources.keySet()) {
+ String resourceName = computeResources.get(id);
+ if (resourceName.equals(stampedeHostName)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ return client.createExperiment(simpleExperiment);
+ }
+ }
+ }
+ } catch (AiravataSystemException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataSystemException(e);
+ } catch (InvalidRequestException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new InvalidRequestException(e);
+ } catch (AiravataClientException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataClientException(e);
+ } catch (TException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new TException(e);
+ }
+ return null;
+ }
+
+ public static String createExperimentNWCHEMStampede(Airavata.Client client) throws TException {
+ try {
+ List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
+ InputDataObjectType input = new InputDataObjectType();
+ input.setName("Water_Molecule_Input");
+ input.setType(DataType.URI);
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/NWCHEM_FILES/water.nw");
+
+ exInputs.add(input);
+
+ List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
+ OutputDataObjectType output = new OutputDataObjectType();
+ output.setName("NWChem_Execution_Log");
+ output.setType(DataType.URI);
+ output.setValue("");
+
+ exOut.add(output);
+
+ Experiment simpleExperiment =
+ ExperimentModelUtil.createSimpleExperiment("default", "admin", "NWchemExperiment", "Testing", nwchemAppId, exInputs);
+ simpleExperiment.setExperimentOutputs(exOut);
+
+ Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(nwchemAppId);
+ if (computeResources != null && computeResources.size() != 0) {
+ for (String id : computeResources.keySet()) {
+ String resourceName = computeResources.get(id);
+ if (resourceName.equals(stampedeHostName)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ return client.createExperiment(simpleExperiment);
+ }
+ }
+ }
+ } catch (AiravataSystemException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataSystemException(e);
+ } catch (InvalidRequestException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new InvalidRequestException(e);
+ } catch (AiravataClientException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataClientException(e);
+ } catch (TException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new TException(e);
+ }
+ return null;
+ }
+ public static String createExperimentAUTODOCKStampede(Airavata.Client client) throws TException {
+ try {
+ List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
+ InputDataObjectType input = new InputDataObjectType();
+ input.setName("AD4_parameters.dat");
+ input.setType(DataType.URI);
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/AD4_parameters.dat");
+
+ InputDataObjectType input1 = new InputDataObjectType();
+ input1.setName("hsg1.A.map");
+ input1.setType(DataType.URI);
+ input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.A.map");
+
+ InputDataObjectType input2 = new InputDataObjectType();
+ input2.setName("hsg1.C.map");
+ input2.setType(DataType.URI);
+ input2.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.C.map");
+
+ InputDataObjectType input3 = new InputDataObjectType();
+ input3.setName("hsg1.d.map");
+ input3.setType(DataType.URI);
+ input3.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.d.map");
+
+ InputDataObjectType input4 = new InputDataObjectType();
+ input4.setName("hsg1.e.map");
+ input4.setType(DataType.URI);
+ input4.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.e.map");
+
+ InputDataObjectType input5 = new InputDataObjectType();
+ input5.setName("hsg1.HD.map");
+ input5.setType(DataType.URI);
+ input5.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.HD.map");
+
+ InputDataObjectType input6 = new InputDataObjectType();
+ input6.setName("hsg1.maps.fld");
+ input6.setType(DataType.URI);
+ input6.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.maps.fld");
+
+ InputDataObjectType input7 = new InputDataObjectType();
+ input7.setName("hsg1.NA.map");
+ input7.setType(DataType.URI);
+ input7.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.NA.map");
+
+ InputDataObjectType input8 = new InputDataObjectType();
+ input8.setName("hsg1.N.map");
+ input8.setType(DataType.URI);
+ input8.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.N.map");
+
+ InputDataObjectType input9 = new InputDataObjectType();
+ input9.setName("hsg1.OA.map");
+ input9.setType(DataType.URI);
+ input9.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.OA.map");
+
+ InputDataObjectType input10 = new InputDataObjectType();
+ input10.setName("ind.dpf");
+ input10.setType(DataType.URI);
+ input10.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/ind.dpf");
+
+ InputDataObjectType input11 = new InputDataObjectType();
+ input11.setName("ind.pdbqt");
+ input11.setType(DataType.URI);
+ input11.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/ind.pdbqt");
+
+
+ exInputs.add(input);
+ exInputs.add(input1);
+ exInputs.add(input2);
+ exInputs.add(input3);
+ exInputs.add(input4);
+ exInputs.add(input5);
+ exInputs.add(input6);
+ exInputs.add(input7);
+ exInputs.add(input8);
+ exInputs.add(input9);
+ exInputs.add(input10);
+ exInputs.add(input11);
+
+ List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
+ OutputDataObjectType output = new OutputDataObjectType();
+ output.setName("ind.dlg");
+ output.setType(DataType.URI);
+ output.setValue("");
+
+ OutputDataObjectType output1 = new OutputDataObjectType();
+ output1.setName("Autodock.oJobID");
+ output1.setType(DataType.URI);
+ output1.setValue("");
+
+ exOut.add(output);
+ exOut.add(output1);
+
+ Experiment simpleExperiment =
+ ExperimentModelUtil.createSimpleExperiment("default", "admin", "AutoDockExperiment", "Testing", autodockAppId, exInputs);
+ simpleExperiment.setExperimentOutputs(exOut);
+
+ Map<String, String> computeResources = airavataClient.getAvailableAppInterfaceComputeResources(autodockAppId);
+ if (computeResources != null && computeResources.size() != 0) {
+ for (String id : computeResources.keySet()) {
+ String resourceName = computeResources.get(id);
+ if (resourceName.equals(stampedeHostName)) {
+ ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
+ UserConfigurationData userConfigurationData = new UserConfigurationData();
+ userConfigurationData.setAiravataAutoSchedule(false);
+ userConfigurationData.setOverrideManualScheduledParams(false);
+ userConfigurationData.setComputationalResourceScheduling(scheduling);
+ simpleExperiment.setUserConfigurationData(userConfigurationData);
+ return client.createExperiment(simpleExperiment);
+ }
+ }
+ }
+ } catch (AiravataSystemException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataSystemException(e);
+ } catch (InvalidRequestException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new InvalidRequestException(e);
+ } catch (AiravataClientException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new AiravataClientException(e);
+ } catch (TException e) {
+ logger.error("Error occured while creating the experiment...", e.getMessage());
+ throw new TException(e);
+ }
+ return null;
+ }
+
public static String createExperimentWRFTrestles(Airavata.Client client) throws TException {
try {
List<InputDataObjectType> exInputs = new ArrayList<InputDataObjectType>();
InputDataObjectType input = new InputDataObjectType();
input.setName("WRF_Namelist");
input.setType(DataType.URI);
- input.setValue("/Users/chathuri/Downloads/wrf_sample_inputs/namelist.input");
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/namelist.input");
InputDataObjectType input1 = new InputDataObjectType();
input1.setName("WRF_Input_File");
input1.setType(DataType.URI);
- input1.setValue("/Users/chathuri/Downloads/wrf_sample_inputs/wrfinput_d01");
+ input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfinput_d01");
InputDataObjectType input2 = new InputDataObjectType();
input2.setName("WRF_Boundary_File");
input2.setType(DataType.URI);
- input2.setValue("/Users/chathuri/Downloads/wrf_sample_inputs/wrfbdy_d01");
+ input2.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfbdy_d01");
exInputs.add(input);
exInputs.add(input1);
@@ -812,19 +1317,19 @@ public class CreateLaunchExperiment {
InputDataObjectType input = new InputDataObjectType();
input.setName("Heat_Restart_File");
input.setType(DataType.URI);
- input.setValue("/Users/lahirugunathilake/Downloads/02_Heat.rst");
+ input.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AMBER_FILES/02_Heat.rst");
exInputs.add(input);
InputDataObjectType input1 = new InputDataObjectType();
input1.setName("Production_Control_File");
input1.setType(DataType.URI);
- input1.setValue("/Users/lahirugunathilake/Downloads/03_Prod.in");
+ input1.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AMBER_FILES/03_Prod.in");
exInputs.add(input1);
InputDataObjectType input2 = new InputDataObjectType();
input2.setName("Parameter_Topology_File");
input2.setType(DataType.URI);
- input2.setValue("/Users/lahirugunathilake/Downloads/prmtop");
+ input2.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AMBER_FILES/prmtop");
exInputs.add(input2);
List<OutputDataObjectType> exOut = new ArrayList<OutputDataObjectType>();
[2/2] airavata git commit: Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Posted by sh...@apache.org.
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d3aff435
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d3aff435
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d3aff435
Branch: refs/heads/master
Commit: d3aff435ef9b832313f7accba02b0f8d5b313bb5
Parents: 3eacfb8 2330ad8
Author: shamrath <sh...@gmail.com>
Authored: Fri Nov 14 15:24:37 2014 -0500
Committer: shamrath <sh...@gmail.com>
Committed: Fri Nov 14 15:24:37 2014 -0500
----------------------------------------------------------------------
.../airavata/client/samples/CreateLaunchExperimentUS3.java | 6 +++---
.../airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
----------------------------------------------------------------------