Protege Server Will Not Start

Post Reply
bwilliams
Posts: 6
Joined: 07 Jun 2013, 20:21

Hello everyone,

After working through several start-up errors with protege server, I am now confronted with one that I can't make heads or tails of.

Essentially, you just start Protege Server ./run_protege_server.sh

it loads up the project, but just as soon as the project is loaded protege barfs.

I've attached the log file.

I'm running:
Centos 6
Protege 3.4.8
Essential 4
java-1.6.0-openjdk

Thanks,
Barry
bwilliams
Posts: 6
Joined: 07 Jun 2013, 20:21

I forgot to mention that I am using SQLfire as my DB
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

Hi Barry,

Unfortunately, the log file has not been attached to your post. You could post the relevant lines from the log files into a reply here - it shouldn't be too big.

Things to check for:

- You have configured the metaproject correctly and the path to the project file (.PPRJ) is correct. As we can't tell where you want to store your repository, the out-of-the-box metaproject.pprj does not have the PATH to the project file set.

- You have enough maximum memory available for the Protege server. Use the MAX_MEMORY parameter in the run_protege_server.sh file. By default, this is 500MB but you're likely to need this to 1024MB or 2048MB

- Have you used a database to persist the repository? If so, make sure that Protege can find the required JDBC driver.

Hope this helps

Jonathan
Essential Project Team
bwilliams
Posts: 6
Joined: 07 Jun 2013, 20:21

Ok, maybe I'm not seeing it, but I can't see the log file I attached to the original post. Here is it's contents:

2013.06.07 15:56:06.284 EDT INFO: *** SYSTEM START *** -- Server.startServer()
2013.06.07 15:56:06.288 EDT INFO: Protege server is starting... -- Server.startServer()
2013.06.07 15:56:06.288 EDT CONFIG: Protege 3.4.8 Build 629, JVM 1.6.0_24-b24, memory=506M, Linux, encoding=UTF-8, language=en, country=US -- SystemUtilities.logSystemInfo()
2013.06.07 15:56:06.331 EDT CONFIG: Server port = 5200, registry port = 1099, compressed stream -- RmiSocketFactory.reportPorts()
2013.06.07 15:56:06.395 EDT INFO: Using metaproject from: file:/usr/local/EssentialArchitectureManager/essential_metamodel/metaproject.pprj -- Server.initialize()
2013.06.07 15:56:07.733 EDT INFO: Loading project Essential AM Annotations from file:/usr/local/EssentialArchitectureManager/essential_metamodel/annotation_metaproject.pprj -- Server.createProject()
2013.06.07 15:56:08.847 EDT INFO: Loading project Essential AM Respository from file:/usr/local/EssentialArchitectureManager/essential_metamodel/essential_baseline_v4.0.pprj -- Server.createProject()
2013.06.07 15:56:10.240 EDT INFO: Loaded 5000 instances: essential_baseline_v1.2_ProjectKB_Class1854 -- Parser.getInstance()
2013.06.07 15:56:10.810 EDT INFO: Loaded 6000 instances: essential_baseline_v1.2_ProjectKB_Class19563 -- Parser.getInstance()
2013.06.07 15:56:11.274 EDT INFO: Loaded 7000 instances: essential_baseline_v1_ProjectKB_Class1837 -- Parser.getInstance()
2013.06.07 15:56:11.721 EDT INFO: Loaded 8000 instances: essential_baseline_v1_ProjectKB_Instance_21330 -- Parser.getInstance()
2013.06.07 15:56:11.750 EDT INFO: Set type on 5000 instances: essential_baseline_v1_ProjectKB_Instance_21368 -- Parser.getInstance()
2013.06.07 15:56:12.298 EDT INFO: Loaded 9000 instances: essential_baseline_v1_ProjectKB_Instance_24311 -- Parser.getInstance()
2013.06.07 15:56:12.425 EDT INFO: Set type on 6000 instances: essential_baseline_v1_ProjectKB_Instance_24566 -- Parser.getInstance()
2013.06.07 15:56:12.713 EDT INFO: Loaded 10000 instances: essential_baseline_v1_ProjectKB_Instance_30526 -- Parser.getInstance()
2013.06.07 15:56:12.819 EDT INFO: Set type on 7000 instances: essential_baseline_v1_ProjectKB_Instance_31201 -- Parser.getInstance()
2013.06.07 15:56:12.939 EDT INFO: Loaded 11000 instances: essential_baseline_v1_ProjectKB_Instance_31731 -- Parser.getInstance()
2013.06.07 15:56:13.100 EDT INFO: Set type on 8000 instances: essential_baseline_v1_ProjectKB_Instance_35082 -- Parser.getInstance()
2013.06.07 15:56:13.335 EDT INFO: Loaded 12000 instances: essential_baseline_v1_ProjectKB_Instance_35229 -- Parser.getInstance()
2013.06.07 15:56:13.508 EDT INFO: Loaded 13000 instances: essential_baseline_v3.5_ProjectKB_Class14596 -- Parser.getInstance()
2013.06.07 15:56:13.536 EDT INFO: Set type on 9000 instances: essential_baseline_v1_ProjectKB_Instance_42428 -- Parser.getInstance()
2013.06.07 15:56:13.717 EDT INFO: Loaded 14000 instances: essential_baseline_v1_ProjectKB_Instance_46807 -- Parser.getInstance()
2013.06.07 15:56:13.776 EDT INFO: Set type on 10000 instances: essential_baseline_v1_ProjectKB_Instance_4710 -- Parser.getInstance()
2013.06.07 15:56:13.916 EDT INFO: Loaded 15000 instances: essential_baseline_v1_ProjectKB_Instance_49888 -- Parser.getInstance()
2013.06.07 15:56:14.000 EDT INFO: Set type on 11000 instances: essential_baseline_v1_ProjectKB_Instance_53906 -- Parser.getInstance()
2013.06.07 15:56:14.114 EDT INFO: Loaded 16000 instances: essential_baseline_v1_ProjectKB_Instance_56281 -- Parser.getInstance()
2013.06.07 15:56:14.220 EDT INFO: Set type on 12000 instances: essential_baseline_v1_ProjectKB_Instance_5714 -- Parser.getInstance()
2013.06.07 15:56:14.289 EDT INFO: Loaded 17000 instances: essential_baseline_v4.0_ProjectKB_Class26656 -- Parser.getInstance()
2013.06.07 15:56:14.489 EDT INFO: Set type on 13000 instances: essential_baseline_v1_ProjectKB_Instance_59894 -- Parser.getInstance()
2013.06.07 15:56:14.530 EDT INFO: Loaded 18000 instances: essential_baseline_v3.0.3_ProjectKB_Class36789 -- Parser.getInstance()
2013.06.07 15:56:14.616 EDT INFO: Set type on 14000 instances: essential_baseline_v1_ProjectKB_Instance_68117 -- Parser.getInstance()
2013.06.07 15:56:14.633 EDT INFO: Loaded 19000 instances: essential_baseline_v1_ProjectKB_Instance_6899 -- Parser.getInstance()
2013.06.07 15:56:14.744 EDT INFO: Set type on 15000 instances: essential_baseline_v1_ProjectKB_Instance_8342 -- Parser.getInstance()
2013.06.07 15:56:14.745 EDT INFO: Loaded 20000 instances: essential_baseline_v1_ProjectKB_Instance_8369 -- Parser.getInstance()
2013.06.07 15:56:14.835 EDT INFO: Loaded 21000 instances: essential_baseline_v2.0_ProjectKB_Class11039 -- Parser.getInstance()
2013.06.07 15:56:14.864 EDT INFO: Set type on 16000 instances: essential_baseline_v2.0_ProjectKB_Class115038 -- Parser.getInstance()
2013.06.07 15:56:14.926 EDT INFO: Loaded 22000 instances: essential_baseline_v2.0_ProjectKB_Class12153 -- Parser.getInstance()
2013.06.07 15:56:14.959 EDT INFO: Set type on 17000 instances: essential_baseline_v2.0_ProjectKB_Class12592 -- Parser.getInstance()
2013.06.07 15:56:14.976 EDT INFO: Loaded 23000 instances: essential_baseline_v2.0_ProjectKB_Class135952 -- Parser.getInstance()
2013.06.07 15:56:15.061 EDT INFO: Set type on 18000 instances: essential_baseline_v2.0_ProjectKB_Class136446 -- Parser.getInstance()
2013.06.07 15:56:15.081 EDT INFO: Loaded 24000 instances: essential_baseline_v2.0_ProjectKB_Class145287 -- Parser.getInstance()
2013.06.07 15:56:15.096 EDT INFO: Set type on 19000 instances: essential_baseline_v2.0_ProjectKB_Class16072 -- Parser.getInstance()
2013.06.07 15:56:15.112 EDT INFO: Loaded 25000 instances: essential_baseline_v2.0_ProjectKB_Class21916 -- Parser.getInstance()
2013.06.07 15:56:15.130 EDT INFO: Set type on 20000 instances: essential_baseline_v2.0_ProjectKB_Class22571 -- Parser.getInstance()
2013.06.07 15:56:15.142 EDT INFO: Loaded 26000 instances: essential_baseline_v2.0_ProjectKB_Class22981 -- Parser.getInstance()
2013.06.07 15:56:15.164 EDT INFO: Set type on 21000 instances: essential_baseline_v2.0_ProjectKB_Class26579 -- Parser.getInstance()
2013.06.07 15:56:15.175 EDT INFO: Loaded 27000 instances: essential_baseline_v2.0_ProjectKB_Class27251 -- Parser.getInstance()
2013.06.07 15:56:15.194 EDT INFO: Set type on 22000 instances: essential_baseline_v2.0_ProjectKB_Class27868 -- Parser.getInstance()
2013.06.07 15:56:15.207 EDT INFO: Loaded 28000 instances: essential_baseline_v2.0_ProjectKB_Class28442 -- Parser.getInstance()
2013.06.07 15:56:15.227 EDT INFO: Set type on 23000 instances: essential_baseline_v2.0_ProjectKB_Class29104 -- Parser.getInstance()
2013.06.07 15:56:15.577 EDT INFO: Loaded 29000 instances: essential_baseline_v2.0_ProjectKB_Class2970 -- Parser.getInstance()
2013.06.07 15:56:15.597 EDT INFO: Set type on 24000 instances: essential_baseline_v2.0_ProjectKB_Class31997 -- Parser.getInstance()
2013.06.07 15:56:15.609 EDT INFO: Loaded 30000 instances: essential_baseline_v2.0_ProjectKB_Class3899 -- Parser.getInstance()
2013.06.07 15:56:15.634 EDT INFO: Set type on 25000 instances: essential_baseline_v2.0_ProjectKB_Class42331 -- Parser.getInstance()
2013.06.07 15:56:15.644 EDT INFO: Loaded 31000 instances: essential_baseline_v2.0_ProjectKB_Class4451 -- Parser.getInstance()
2013.06.07 15:56:15.670 EDT INFO: Set type on 26000 instances: essential_baseline_v2.0_ProjectKB_Class46007 -- Parser.getInstance()
2013.06.07 15:56:15.675 EDT INFO: Loaded 32000 instances: essential_baseline_v2.0_ProjectKB_Class46185 -- Parser.getInstance()
2013.06.07 15:56:15.704 EDT INFO: Set type on 27000 instances: essential_baseline_v2.0_ProjectKB_Class47029 -- Parser.getInstance()
2013.06.07 15:56:15.709 EDT INFO: Loaded 33000 instances: essential_baseline_v2.0_ProjectKB_Class4741 -- Parser.getInstance()
2013.06.07 15:56:15.737 EDT INFO: Set type on 28000 instances: essential_baseline_v2.0_ProjectKB_Class52211 -- Parser.getInstance()
2013.06.07 15:56:15.739 EDT INFO: Loaded 34000 instances: essential_baseline_v2.0_ProjectKB_Class52324 -- Parser.getInstance()
2013.06.07 15:56:15.768 EDT INFO: Set type on 29000 instances: essential_baseline_v2.0_ProjectKB_Class5964 -- Parser.getInstance()
2013.06.07 15:56:15.772 EDT INFO: Loaded 35000 instances: essential_baseline_v2.0_ProjectKB_Class60677 -- Parser.getInstance()
2013.06.07 15:56:15.809 EDT INFO: Set type on 30000 instances: essential_baseline_v2.0_ProjectKB_Class6569 -- Parser.getInstance()
2013.06.07 15:56:15.818 EDT INFO: Loaded 36000 instances: essential_baseline_v2.0_ProjectKB_Class6817 -- Parser.getInstance()
2013.06.07 15:56:15.843 EDT INFO: Set type on 31000 instances: essential_baseline_v2.0_ProjectKB_Class7359 -- Parser.getInstance()
2013.06.07 15:56:15.852 EDT INFO: Loaded 37000 instances: essential_baseline_v2.0_ProjectKB_Class7663 -- Parser.getInstance()
2013.06.07 15:56:15.875 EDT INFO: Set type on 32000 instances: essential_baseline_v2.0_ProjectKB_Class8339 -- Parser.getInstance()
2013.06.07 15:56:15.887 EDT INFO: Loaded 38000 instances: essential_baseline_v2.0_ProjectKB_Class8782 -- Parser.getInstance()
2013.06.07 15:56:15.906 EDT INFO: Set type on 33000 instances: essential_baseline_v2.0_ProjectKB_Class9385 -- Parser.getInstance()
2013.06.07 15:56:15.920 EDT INFO: Loaded 39000 instances: essential_baseline_v2.0_ProjectKB_Class9641 -- Parser.getInstance()
2013.06.07 15:56:16.107 EDT INFO: Set type on 34000 instances: essential_baseline_v3.0.2_ProjectKB_Class4025 -- Parser.getInstance()
2013.06.07 15:56:16.121 EDT INFO: Loaded 40000 instances: essential_baseline_v3.0.3_ProjectKB_Class11069 -- Parser.getInstance()
2013.06.07 15:56:16.144 EDT INFO: Loaded 41000 instances: essential_baseline_v3.0.3_ProjectKB_Class2051 -- Parser.getInstance()
2013.06.07 15:56:16.145 EDT INFO: Set type on 35000 instances: essential_baseline_v3.0.3_ProjectKB_Class2077 -- Parser.getInstance()
2013.06.07 15:56:16.171 EDT INFO: Loaded 42000 instances: essential_baseline_v3.0.3_ProjectKB_Class72048 -- Parser.getInstance()
2013.06.07 15:56:16.188 EDT INFO: Set type on 36000 instances: essential_baseline_v3.0.4_ProjectKB_Class10102 -- Parser.getInstance()
2013.06.07 15:56:16.204 EDT INFO: Loaded 43000 instances: essential_baseline_v3.0.4_ProjectKB_Class10704 -- Parser.getInstance()
2013.06.07 15:56:16.233 EDT INFO: Set type on 37000 instances: essential_baseline_v3.0.4_ProjectKB_Class12585 -- Parser.getInstance()
2013.06.07 15:56:16.238 EDT INFO: Loaded 44000 instances: essential_baseline_v3.0.4_ProjectKB_Class12714 -- Parser.getInstance()
2013.06.07 15:56:16.266 EDT INFO: Set type on 38000 instances: essential_baseline_v3.0.4_ProjectKB_Class13608 -- Parser.getInstance()
2013.06.07 15:56:16.271 EDT INFO: Loaded 45000 instances: essential_baseline_v3.0.4_ProjectKB_Class13752 -- Parser.getInstance()
2013.06.07 15:56:16.284 EDT INFO: Loaded 46000 instances: essential_baseline_v3.0.4_ProjectKB_Class16352 -- Parser.getInstance()
2013.06.07 15:56:16.294 EDT INFO: Loaded 47000 instances: essential_baseline_v3.0.4_ProjectKB_Class13932 -- Parser.getInstance()
2013.06.07 15:56:16.322 EDT INFO: Set type on 39000 instances: essential_baseline_v3.0.4_ProjectKB_Class14637 -- Parser.getInstance()
2013.06.07 15:56:16.335 EDT INFO: Loaded 48000 instances: essential_baseline_v3.0.4_ProjectKB_Class15015 -- Parser.getInstance()
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2013.06.07 15:56:16.384 EDT INFO: Set type on 41000 instances: essential_baseline_v3.0.4_ProjectKB_Class16682 -- Parser.getInstance()
2013.06.07 15:56:16.414 EDT INFO: Loaded 49000 instances: essential_baseline_v3.0.4_ProjectKB_Class2362 -- Parser.getInstance()
2013.06.07 15:56:16.447 EDT INFO: Loaded 50000 instances: essential_baseline_v3.0.4_ProjectKB_Class3602 -- Parser.getInstance()
2013.06.07 15:56:16.459 EDT INFO: Set type on 42000 instances: essential_baseline_v3.0.4_ProjectKB_Class4090 -- Parser.getInstance()
2013.06.07 15:56:16.613 EDT INFO: Loaded 51000 instances: essential_baseline_v3.0.4_ProjectKB_Class4674 -- Parser.getInstance()
2013.06.07 15:56:16.639 EDT INFO: Loaded 52000 instances: essential_baseline_v3.0.4_ProjectKB_Class5770 -- Parser.getInstance()
2013.06.07 15:56:16.667 EDT INFO: Loaded 53000 instances: essential_baseline_v3.0.4_ProjectKB_Class6823 -- Parser.getInstance()
2013.06.07 15:56:16.701 EDT INFO: Loaded 54000 instances: essential_baseline_v3.0.4_ProjectKB_Class8522 -- Parser.getInstance()
2013.06.07 15:56:16.712 EDT INFO: Set type on 43000 instances: essential_baseline_v3.0.4_ProjectKB_Class8940 -- Parser.getInstance()
2013.06.07 15:56:16.737 EDT INFO: Loaded 55000 instances: essential_baseline_v3.0.4_ProjectKB_Class9563 -- Parser.getInstance()
2013.06.07 15:56:16.759 EDT INFO: Set type on 44000 instances: essential_baseline_v3.0.6_ProjectKB_Class19827 -- Parser.getInstance()
2013.06.07 15:56:16.771 EDT INFO: Loaded 56000 instances: essential_baseline_v3.0.6_ProjectKB_Class20128 -- Parser.getInstance()
2013.06.07 15:56:16.797 EDT INFO: Set type on 45000 instances: essential_baseline_v3.0.6_ProjectKB_Class20842 -- Parser.getInstance()
2013.06.07 15:56:16.807 EDT INFO: Loaded 57000 instances: essential_baseline_v3.0_ProjectKB_Class16795 -- Parser.getInstance()
2013.06.07 15:56:16.833 EDT INFO: Set type on 46000 instances: essential_baseline_v3.0_ProjectKB_Class17620 -- Parser.getInstance()
2013.06.07 15:56:16.841 EDT INFO: Loaded 58000 instances: essential_baseline_v3.0_ProjectKB_Class1864 -- Parser.getInstance()
2013.06.07 15:56:16.871 EDT INFO: Set type on 47000 instances: essential_baseline_v3.0_ProjectKB_Class22675 -- Parser.getInstance()
2013.06.07 15:56:16.880 EDT INFO: Loaded 59000 instances: essential_baseline_v3.0_ProjectKB_Class22945 -- Parser.getInstance()
2013.06.07 15:56:16.908 EDT INFO: Set type on 48000 instances: essential_baseline_v3.0_ProjectKB_Class23712 -- Parser.getInstance()
2013.06.07 15:56:16.918 EDT INFO: Loaded 60000 instances: essential_baseline_v3.0_ProjectKB_Class23997 -- Parser.getInstance()
2013.06.07 15:56:16.947 EDT INFO: Set type on 49000 instances: essential_baseline_v3.0_ProjectKB_Class24863 -- Parser.getInstance()
2013.06.07 15:56:16.964 EDT INFO: Loaded 61000 instances: essential_baseline_v3.0_ProjectKB_Class25205 -- Parser.getInstance()
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2013.06.07 15:56:17.680 EDT INFO: Loaded 62000 instances: essential_baseline_v3.0_ProjectKB_Class26335 -- Parser.getInstance()
2013.06.07 15:56:17.702 EDT INFO: Set type on 51000 instances: essential_baseline_v3.0_ProjectKB_Class27019 -- Parser.getInstance()
2013.06.07 15:56:17.718 EDT INFO: Loaded 63000 instances: essential_baseline_v3.0_ProjectKB_Class27489 -- Parser.getInstance()
2013.06.07 15:56:17.740 EDT INFO: Set type on 52000 instances: essential_baseline_v3.5_ProjectKB_Class10503 -- Parser.getInstance()
2013.06.07 15:56:17.757 EDT INFO: Loaded 64000 instances: essential_baseline_v3.5_ProjectKB_Class10960 -- Parser.getInstance()
2013.06.07 15:56:17.777 EDT INFO: Set type on 53000 instances: essential_baseline_v3.5_ProjectKB_Class11518 -- Parser.getInstance()
2013.06.07 15:56:17.794 EDT INFO: Loaded 65000 instances: essential_baseline_v3.5_ProjectKB_Class11975 -- Parser.getInstance()
2013.06.07 15:56:17.817 EDT INFO: Set type on 54000 instances: essential_baseline_v3.5_ProjectKB_Class12568 -- Parser.getInstance()
2013.06.07 15:56:17.835 EDT INFO: Loaded 66000 instances: essential_baseline_v3.5_ProjectKB_Class12996 -- Parser.getInstance()
2013.06.07 15:56:17.857 EDT INFO: Set type on 55000 instances: essential_baseline_v3.5_ProjectKB_Class13594 -- Parser.getInstance()
2013.06.07 15:56:17.874 EDT INFO: Loaded 67000 instances: essential_baseline_v3.5_ProjectKB_Class14045 -- Parser.getInstance()
2013.06.07 15:56:17.895 EDT INFO: Set type on 56000 instances: essential_baseline_v3.5_ProjectKB_Class14628 -- Parser.getInstance()
2013.06.07 15:56:17.916 EDT INFO: Loaded 68000 instances: essential_baseline_v3.5_ProjectKB_Class2343 -- Parser.getInstance()
2013.06.07 15:56:17.931 EDT INFO: Set type on 57000 instances: essential_baseline_v3.5_ProjectKB_Class2753 -- Parser.getInstance()
2013.06.07 15:56:17.965 EDT INFO: Loaded 69000 instances: essential_baseline_v3.5_ProjectKB_Class3352 -- Parser.getInstance()
2013.06.07 15:56:17.981 EDT INFO: Set type on 58000 instances: essential_baseline_v3.5_ProjectKB_Class3770 -- Parser.getInstance()
2013.06.07 15:56:18.003 EDT INFO: Loaded 70000 instances: essential_baseline_v3.5_ProjectKB_Class4379 -- Parser.getInstance()
2013.06.07 15:56:18.018 EDT INFO: Set type on 59000 instances: essential_baseline_v3.5_ProjectKB_Class4793 -- Parser.getInstance()
2013.06.07 15:56:18.043 EDT INFO: Loaded 71000 instances: essential_baseline_v3.5_ProjectKB_Class5412 -- Parser.getInstance()
2013.06.07 15:56:18.061 EDT INFO: Set type on 60000 instances: essential_baseline_v3.5_ProjectKB_Class5816 -- Parser.getInstance()
2013.06.07 15:56:18.084 EDT INFO: Loaded 72000 instances: essential_baseline_v3.5_ProjectKB_Class6435 -- Parser.getInstance()
2013.06.07 15:56:18.100 EDT INFO: Set type on 61000 instances: essential_baseline_v3.5_ProjectKB_Class6837 -- Parser.getInstance()
2013.06.07 15:56:18.123 EDT INFO: Loaded 73000 instances: essential_baseline_v3.5_ProjectKB_Class7457 -- Parser.getInstance()
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2013.06.07 15:56:18.161 EDT INFO: Loaded 74000 instances: essential_baseline_v3.5_ProjectKB_Class8466 -- Parser.getInstance()
2013.06.07 15:56:18.178 EDT INFO: Set type on 63000 instances: essential_baseline_v3.5_ProjectKB_Class8867 -- Parser.getInstance()
2013.06.07 15:56:18.200 EDT INFO: Loaded 75000 instances: essential_baseline_v3.5_ProjectKB_Class9474 -- Parser.getInstance()
2013.06.07 15:56:18.219 EDT INFO: Set type on 64000 instances: essential_baseline_v3.5_ProjectKB_Class9879 -- Parser.getInstance()
2013.06.07 15:56:18.261 EDT INFO: Set type on 65000 instances: essential_baseline_v4.0_ProjectKB_Class22679 -- Parser.getInstance()
2013.06.07 15:56:18.283 EDT INFO: Loaded 76000 instances: essential_baseline_v4.0_ProjectKB_Class23080 -- Parser.getInstance()
2013.06.07 15:56:18.314 EDT INFO: Set type on 66000 instances: essential_baseline_v4.0_ProjectKB_Class25962 -- Parser.getInstance()
2013.06.07 15:56:18.346 EDT INFO: Loaded 77000 instances: essential_baseline_v4.0_ProjectKB_Class26614 -- Parser.getInstance()
2013.06.07 15:56:18.363 EDT INFO: Set type on 67000 instances: essential_baseline_v4.0_ProjectKB_Class26972 -- Parser.getInstance()
2013.06.07 15:56:18.413 EDT INFO: Set type on 68000 instances: essential_baseline_v4.0_ProjectKB_Class33440 -- Parser.getInstance()
2013.06.07 15:56:18.418 EDT INFO: Loaded 78000 instances: essential_baseline_v4.0_ProjectKB_Class33517 -- Parser.getInstance()
2013.06.07 15:56:18.473 EDT INFO: Set type on 69000 instances: essential_prj_AA_v1.2_graphArchTest_ProjectKB_Instance_3776 -- Parser.getInstance()
2013.06.07 15:56:18.476 EDT INFO: Loaded 79000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_30068 -- Parser.getInstance()
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2013.06.07 15:56:18.845 EDT INFO: Loaded 80000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_141413 -- Parser.getInstance()
2013.06.07 15:56:18.894 EDT INFO: Set type on 71000 instances: essential_prj_CC_v1.4.2_ProjectKB_Instance_191176 -- Parser.getInstance()
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2013.06.07 15:56:18.951 EDT INFO: Set type on 72000 instances: viewer3_dev_12032012_ProjectKB_Class11906 -- Parser.getInstance()
2013.06.07 15:56:18.967 EDT INFO: Loaded 82000 instances: viewer3_dev_12032012_ProjectKB_Class12241 -- Parser.getInstance()
2013.06.07 15:56:19.021 EDT INFO: Set type on 73000 instances: viewer3_dev_12032012_ProjectKB_Class13418 -- Parser.getInstance()
2013.06.07 15:56:19.060 EDT INFO: Loaded 83000 instances: viewer3_dev_12032012_ProjectKB_Class17246 -- Parser.getInstance()
2013.06.07 15:56:19.092 EDT INFO: Set type on 74000 instances: viewer3_dev_12032012_ProjectKB_Class18930 -- Parser.getInstance()
2013.06.07 15:56:22.966 EDT INFO: Loading project plugins for project Essential AM Annotations -- Server.afterLoad()
2013.06.07 15:56:22.977 EDT INFO: Loading project plugins for project Essential AM Respository -- Server.afterLoad()
2013.06.07 15:56:23.035 EDT SEVERE: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:419)
at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:267)
at sun.rmi.transport.Transport$1.run(Transport.java:177)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:679)
at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:273)
at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:251)
at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:377)
at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
at edu.stanford.smi.protege.server.Server.main(Unknown Source)
Caused by: java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
at sun.rmi.registry.RegistryImpl_Skel.dispatch(Unknown Source)
at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:409)
at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:267)
at sun.rmi.transport.Transport$1.run(Transport.java:177)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:679)
Caused by: java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:266)
at sun.rmi.server.LoaderHandler.loadClass(LoaderHandler.java:451)
at sun.rmi.server.LoaderHandler.loadClass(LoaderHandler.java:182)
at java.rmi.server.RMIClassLoader$2.loadClass(RMIClassLoader.java:637)
at java.rmi.server.RMIClassLoader.loadClass(RMIClassLoader.java:264)
at sun.rmi.server.MarshalInputStream.resolveClass(MarshalInputStream.java:220)
at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1609)
at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1514)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1768)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1347)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:369)
... 12 more
-- Server.bindName()
2013.06.07 15:56:23.036 EDT SEVERE: server startup failed -- java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:419)
at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:267)
at sun.rmi.transport.Transport$1.run(Transport.java:177)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:679)
at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(StreamRemoteCall.java:273)
at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:251)
at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:377)
at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
at edu.stanford.smi.protege.server.Server.main(Unknown Source)
Caused by: java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
at sun.rmi.registry.RegistryImpl_Skel.dispatch(Unknown Source)
at sun.rmi.server.UnicastServerRef.oldDispatch(UnicastServerRef.java:409)
at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:267)
at sun.rmi.transport.Transport$1.run(Transport.java:177)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:679)
Caused by: java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:266)
at sun.rmi.server.LoaderHandler.loadClass(LoaderHandler.java:451)
at sun.rmi.server.LoaderHandler.loadClass(LoaderHandler.java:182)
at java.rmi.server.RMIClassLoader$2.loadClass(RMIClassLoader.java:637)
at java.rmi.server.RMIClassLoader.loadClass(RMIClassLoader.java:264)
at sun.rmi.server.MarshalInputStream.resolveClass(MarshalInputStream.java:220)
at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1609)
at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1514)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1768)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1347)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:369)
... 12 more

2013.06.07 16:02:07.375 EDT WARNING: Exception caught closing connection during cleanup -- java.sql.SQLException: Cannot close a connection while a transaction is still active.
at com.vmware.sqlfire.internal.client.am.SQLExceptionFactory40.getSQLException(SQLExceptionFactory40.java:96)
at com.vmware.sqlfire.internal.client.am.SqlException.getSQLException(SqlException.java:394)
at com.vmware.sqlfire.internal.client.am.Connection.closeResourcesX(Connection.java:1013)
at com.vmware.sqlfire.internal.client.am.Connection.closeX(Connection.java:994)
at com.vmware.sqlfire.internal.client.net.NetConnection.closeX(NetConnection.java:2875)
at com.vmware.sqlfire.internal.client.am.Connection.close(Connection.java:961)
at com.vmware.sqlfire.internal.client.net.NetConnection.close(NetConnection.java:2859)
at com.vmware.sqlfire.internal.client.net.NetConnection40.close(NetConnection40.java:232)
at edu.stanford.smi.protege.storage.database.pool.ConnectionInfo.close(Unknown Source)
at edu.stanford.smi.protege.storage.database.pool.ConnectionPool.cleanup(Unknown Source)
at edu.stanford.smi.protege.storage.database.pool.ConnectionPool.access$000(Unknown Source)
at edu.stanford.smi.protege.storage.database.pool.ConnectionPool$2.run(Unknown Source)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:351)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:178)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:165)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:267)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:679)
Caused by: ERROR 25001: Cannot close a connection while a transaction is still active.
at com.vmware.sqlfire.internal.client.am.Connection.checkForTransactionInProgress(Connection.java:973)
at com.vmware.sqlfire.internal.client.am.Connection.closeResourcesX(Connection.java:1009)
... 17 more
bwilliams
Posts: 6
Joined: 07 Jun 2013, 20:21

I haven't messed with Max memory, but the other two settings (pprj exact locations, and JDBC driver) are good.
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

bwilliams wrote:I forgot to mention that I am using SQLfire as my DB
I'm not sure SQLfire is supported by Protege.
In terms of what is supported, it should be any JDBC-compliant database but we know there are problems with Oracle and DB2. The Protege team run nightly tests against MySQL and PostgreSQL.

Start by running Protege on your CentOS machine in client, stand-alone mode. When you convert your repository to use the Protege Database format did that process succeed? Was Protege able to create and populate the database in SQLfire for the Essential repository?

If all was well in terms of running Protege in stand-alone mode, backed by the SQLfire database, then when running in server mode, it should be able to load the project as long as it can see the JDBC driver and connect to the database.

Jonathan
Essential Project Team
bwilliams
Posts: 6
Joined: 07 Jun 2013, 20:21

Yes, things worked to set up the DB in client mode. Converting the project to a DB project was successful, and the DB was populated - I went in using the DB client to check to see if the tables had anything in them.

So, everything is good as far as setting up the database - to my knowledge.
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

Although there's a database exception in there, which could be at the heart of this, there's a class not found error during the bind to the server.

So, let's try the work-around for the Java RMI issue that appeared in Java 1.6.0-29 and see if that works:

Protege team posting

This Essential forum posting describes our recommended approach, which is to take a copy of protege.jar from the Protege install directory and drop it in the root of your Essential Viewer installation in Tomcat (e.g.<TOMCAT>/webapps/essential_viewer)
Then update the CODEBASE_URL in run_protege_server.sh to point to this protege.jar file in Tomcat via http:

Code: Select all

set CODEBASE_URL=http://localhost:8080/essential_viewer/protege.jar
NOTE: This will require that Tomcat is running before the Protege Server can startup.

Let me know how you get on with this.

Jonathan
Essential Project Team
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

bwilliams wrote:Yes, things worked to set up the DB in client mode. Converting the project to a DB project was successful, and the DB was populated - I went in using the DB client to check to see if the tables had anything in them.

So, everything is good as far as setting up the database - to my knowledge.
Excellent. Sounds like SQLfire is another compatible database.

I think the answer lies in that Java 1.6.0_29 / Java 1.7 issue that the Protege team mention.
Try the workaround to use Tomcat to serve the CODEBASE_URL and the server should then be able to register with the RMI Registry once it's started.

Jonathan
Essential Project Team
bwilliams
Posts: 6
Joined: 07 Jun 2013, 20:21

I saw that workaround. I currently have a basic HTTP server serving that jar file.
the line in run_protege_server.sh is:
CODEBASE_URL=http://ess-app1.wglabs.local:8000/protege.jar

ess-app1.wglabs.local is the name of the local machine. It is not using tomcat to serve it, but rather it is using webfs 1.2

would you recommend I switch to pulling this from tomcat instead?
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

It shouldn't make a difference but it could be worth trying.

This work-around does resolve the ClassNotFoundException during the server binding to RMI Registry.

Let me ask a silly question. :) You do have a copy of the protege.jar file in the root of that other HTTP server and the server is running? That file has to be available at the specified URL for this to work.

I normally recommend using the Essential Viewer install in Tomcat because then you know you have that component there and running.

Jonathan
Essential Project Team
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