AutoDock4 Callgraph Activity Results Problem

AutoDock4 Callgraph Activity Results Problem

Hi All.

I am trying to analyze Autodock4 with VTune on Linux. The compilation & execution of autogrid4 & autodock4 had been succesfull (as I checked both config.log). Now when using Intel VTune to analyze it's CALLGRAPH, I did -

[xxx@n1 bin] $ /opt/intel/vtune/bin/vtl activity autodock-intel -c callgraph -app ./autodock4,"100" -moi ./autodock4 run

which resulted into as -

----

VTune Performance Analyzer 9.0 for Linux*
Copyright (C) 2000-2007 Intel Corporation. All rights reserved.

The Activity has been successfully created.
The Activity is running.
Tue Dec 23 14:25:14 2008 Reading property files started...

Tue Dec 23 14:25:14 2008 Reading property files done.

Tue Dec 23 14:25:14 2008 Static instrumentation started
Tue Dec 23 14:25:15 2008 All functions instrumentation of module "autodock4" was successful.
Tue Dec 23 14:25:15 2008 Exports instrumentation of module "libc-2.3.4.so" was skipped.
Tue Dec 23 14:25:15 2008 All functions instrumentation of module "libcxaguard.so.5" was successful.
Tue Dec 23 14:25:15 2008 Minimal instrumentation of module "libdl-2.3.4.so" was successful.
Tue Dec 23 14:25:15 2008 Exports instrumentation of module "libgcc_s-3.4.6-20060404.so.1" was successful.
Tue Dec 23 14:25:16 2008 All functions instrumentation of module "libimf.so" was successful.
Tue Dec 23 14:25:16 2008 All functions instrumentation of module "libm-2.3.4.so" was skipped.
Tue Dec 23 14:25:17 2008 Exports instrumentation of module "libstdc++.so.6.0.3" was successful.
Tue Dec 23 14:25:17 2008 Static instrumentation done
Tue Dec 23 14:25:17 2008 Data collection started...
Wed Dec 24 00:25:12 2008 Data collection finished...
The Activity has finished running.
---

To check that activity results (r1) has been created or not, I did -
[xxx@n1 bin]$ /opt/intel/vtune/bin/vtl show

which resulted into as -

---
VTune Performance Analyzer 9.0 for Linux*
Copyright (C) 2000-2007 Intel Corporation. All rights reserved.

a1__autodock-intel
---

I don't get activity results (r1) as r1__Call Grapgh

I have following queries -

(a) Why it's takes almost 9-10 hours to generate "Data Collection" information, please check the time when it started & when it completed? I did minimze dpf file as "ga_run 2" when creating an o/p.

(b) The processor configuration is -

processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 15
model name : Intel Xeon CPU X5355 @ 2.66GHz
stepping : 7
cpu MHz : 2666.768
cache size : 4096 KB
physical id : 0
siblings : 4
core id : 0
cpu cores : 4

It has two dies, which means 8 cpu cores.

Why does it takes so much time on 8 core processor?

(c) I had configured & installed Autodock4 with Intel C++ Compiler (v-10.0) as -

./configure --prefix=/home/usr/autodock-intel-compl/prefix CC=/opt/intel/cce/10.0.023/bin/icc CXX=/opt/intel/cce/10.0.023/bin/icpc CCFLAGS=-I/opt/intel/vtune/rdc/analyzer/include LINKFLAGS=/opt/intel/vtune/rdc/analyzer/bin USRLIB=-lVtuneApi

make & make install.

which has been succesfull (as checked in both config.log). The exported libraries path were -

/opt/intel/cce/10.0.023/lib:/opt/intel/vtune/rdc/analyzer/bin

After doing all above why I can't get the activity results (r1)?

(d) To view the summary table of functions, their process, module, thread, & timing information on command-line. I can perform "vtl view a1::r1 -calls -gui" , but without activity (r1), how can I analyze the functions table?

Any clue, if I had missed something?

~BR

11 posts / 0 new
Last post
For more complete information about compiler optimizations, see our Optimization Notice.

I think that VTune Performance Analyzer v9.0 is out of support, now current product is v9.1 Update 1 which has many call graph issues fixed. So please upgrade the product.

To reduce Call graph's overheads, please set other .so modules as "minimal" for Instrumentation Level, and reduce workload for AutoDock4.

Regards, Peter

Quoting - Zhen Yu Wang (Intel)

I think that VTune Performance Analyzer v9.0 is out of support, now current product is v9.1 Update 1 which has many call graph issues fixed. So please upgrade the product.

To reduce Call graph's overheads, please set other .so modules as "minimal" for Instrumentation Level, and reduce workload for AutoDock4.

Regards, Peter

Hi.

I tried the same procedure with LAMMPS(Large-scale Atomic/Molecular Massively Parallel Simulator), it was completely succesfully and I could see the dependency of "lmp_linux" executable on LibVtuneApi.so by doing "ldd lmp_linux".

Similar way, I tried doing for Autogrid4 & Autodock4, why can't I have lVtuneApi.so dependency on these executables when either doing "ldd autogrid4" or "ldd autodock4", rather I see as below -

---

[xxxx@n1 bin]$ ldd autogrid4
libimf.so => /opt/intel/cce/10.0.023/lib/libimf.so (0x0000002a95557000)
libm.so.6 => /lib64/tls/libm.so.6 (0x000000399e600000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000039a0200000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000039a0400000)
libcxaguard.so.5 => /opt/intel/cce/10.0.023/lib/libcxaguard.so.5 (0x0000002a958dc000)
libc.so.6 => /lib64/tls/libc.so.6 (0x000000399e100000)
libdl.so.2 => /lib64/libdl.so.2 (0x000000399e400000)
/lib64/ld-linux-x86-64.so.2 (0x000000399df00000)
--

[xxx@n1 autodock-4.0.1]$ ldd autodock4
libimf.so => /opt/intel/cce/10.0.023/lib/libimf.so (0x0000002a95557000)
libm.so.6 => /lib64/tls/libm.so.6 (0x000000399e600000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000039a0200000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000039a0400000)
libcxaguard.so.5 => /opt/intel/cce/10.0.023/lib/libcxaguard.so.5 (0x0000002a958dc000)
libc.so.6 => /lib64/tls/libc.so.6 (0x000000399e100000)
libdl.so.2 => /lib64/libdl.so.2 (0x000000399e400000)
/lib64/ld-linux-x86-64.so.2 (0x000000399df00000)
---

Please help?

~BR

Hi,

Try another application that we can't prove anything, are you working on v9.1 U1?

If the problem still persists on v9.1 U1, please give URL for downloading Autodock4. Then I will have a try.

Regards, Peter

Quoting - Zhen Yu Wang (Intel)

Hi,

Try another application that we can't prove anything, are you working on v9.1 U1?

If the problem still persists on v9.1 U1, please give URL for downloading Autodock4. Then I will have a try.

Regards, Peter

Hi.

The link for Autodock4 is - http://autodock.scripps.edu/

Please refer above reply, I did say that I had tried LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, http://lammps.sandia.gov/) with Intel VTune-v9.0 and it was completely succesful. I could generate CALLGRAPH for lmp_linux executable of LAMMPS.

If you wish I can help you in generating the same for LAMMPS at your end through this forum or E-mail @ srimks11@gmail.com .

~BR

Quoting - srimks

Hi.

The link for Autodock4 is - http://autodock.scripps.edu/

Please refer above reply, I did say that I had tried LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, http://lammps.sandia.gov/) with Intel VTune-v9.0 and it was completely succesful. I could generate CALLGRAPH for lmp_linux executable of LAMMPS.

If you wish I can help you in generating the same for LAMMPS at your end through this forum or E-mail @ srimks11@gmail.com .

~BR

Thanks for autodock info. Now I have downloaded source, and built it for my platform - Intel64.

#source /opt/intel/cce/10.0.023/bin/iccvars.sh

#./configure CC=icc CXX=icpc

#make & make install

#vtl activity autodock -c callgraph -app ./autodock4,100 -moi ./autodock4 run

Since parameter "100" is big workload, so you can use "kill -12 18717" (autodock_home) in other console, and call graph result can be generated.

[root@conroe-em64t autodock-4.0.1]# vtl show

VTune Performance Analyzer 9.1 for Linux* build 102

Copyright (C) 2000-2008 Intel Corporation. All rights reserved.

a1__autodock

r1___Call Graph Results [127.0.0.1] - Thu Dec 25 12:38:47 2008

Regards, Peter

Quoting - Zhen Yu Wang (Intel)

Quoting - srimks

Hi.

The link for Autodock4 is - http://autodock.scripps.edu/

Please refer above reply, I did say that I had tried LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, http://lammps.sandia.gov/) with Intel VTune-v9.0 and it was completely succesful. I could generate CALLGRAPH for lmp_linux executable of LAMMPS.

If you wish I can help you in generating the same for LAMMPS at your end through this forum or E-mail @ srimks11@gmail.com .

~BR

Thanks for autodock info. Now I have downloaded source, and built it for my platform - Intel64.

#source /opt/intel/cce/10.0.023/bin/iccvars.sh

#./configure CC=icc CXX=icpc

#make & make install

#vtl activity autodock -c callgraph -app ./autodock4,100 -moi ./autodock4 run

Since parameter "100" is big workload, so you can use "kill -12 18717" (autodock_home) in other console, and call graph result can be generated.

[root@conroe-em64t autodock-4.0.1]# vtl show

VTune Performance Analyzer 9.1 for Linux* build 102

Copyright (C) 2000-2008 Intel Corporation. All rights reserved.

a1__autodock

r1___Call Graph Results [127.0.0.1] - Thu Dec 25 12:38:47 2008

Regards, Peter

Hi Peter.

Thanks for your input but I see a peculiar behaviour when using Intel Vtune-v9.1 with moi = 100 & moi=10 as below. In first instance, VTune does instruementation by saying "All functions instrumentation of module "autodock4" was successful" but in second instance with moi=10, I see "All functions instrumentation of module "autodock4" was skipped." . Again, I tried which is not shown below with moi=100 but still it shows "All functions instrumentation of module "autodock4" was skipped.". Check below the command line operation -

----

[xxx@n197 bin]$ /home/user/intel-vtune-9.1/vtune/bin/vtl activity autodock -c callgraph -app ./autodock4,100 -moi ./autodock4 run
VTune Performance Analyzer 9.1 for Linux*. 30 DAY EVALUATION LICENSE build 152
Copyright (C) 2000-2008 Intel Corporation. All rights reserved.

The Activity has been successfully created.
The Activity is running.
Fri Dec 26 09:49:06 2008 Reading property files started...

Fri Dec 26 09:49:07 2008 Reading property files done.

Fri Dec 26 09:49:07 2008 Static instrumentation started
Fri Dec 26 09:49:07 2008 All functions instrumentation of module "autodock4" was successful.
Fri Dec 26 09:49:08 2008 Exports instrumentation of module "libc-2.3.4.so" was successful.
Fri Dec 26 09:49:08 2008 Minimal instrumentation of module "libdl-2.3.4.so" was successful.
Fri Dec 26 09:49:08 2008 Exports instrumentation of module "libgcc_s-3.4.6-20060404.so.1" was successful.
Fri Dec 26 09:49:09 2008 All functions instrumentation of module "libimf.so" was successful.
Fri Dec 26 09:49:09 2008 All functions instrumentation of module "libm-2.3.4.so" was successful.
Fri Dec 26 09:49:10 2008 Exports instrumentation of module "libstdc++.so.6.0.3" was successful.
Fri Dec 26 09:49:10 2008 Static instrumentation done
Fri Dec 26 09:49:10 2008 Data collection started...
Fri Dec 26 09:53:12 2008 Process Call Graph (MT) Data Collection, id "11458", started writing Call Graph data.

Fri Dec 26 09:53:12 2008 Process Call Graph (MT) Data Collection, id "11458", finished writing Call Graph data.

Fri Dec 26 09:53:12 2008 Copying results from remote machine...
Fri Dec 26 09:53:22 2008 Data collection finished...
Fri Dec 26 09:53:22 2008 Updating Call graph database...
Fri Dec 26 09:53:22 2008 Trying to find symbols for module (1 / 7) /home/mukesh/autodock-intel-compl/prefix/bin/autodock4
Fri Dec 26 09:53:22 2008 Succeeded!
Fri Dec 26 09:53:22 2008 Trying to find symbols for module (2 / 7) /apps/intel/cce/11.0.074/lib/intel64/libimf.so
Fri Dec 26 09:53:22 2008 Succeeded!
Fri Dec 26 09:53:22 2008 Trying to find symbols for module (3 / 7) /lib64/libgcc_s.so.1
Fri Dec 26 09:53:23 2008 Succeeded!
Fri Dec 26 09:53:23 2008 Trying to find symbols for module (4 / 7) /lib64/libdl.so.2
Fri Dec 26 09:53:23 2008 Succeeded!
Fri Dec 26 09:53:23 2008 Trying to find symbols for module (5 / 7) /lib64/ld-2.3.4.so
Fri Dec 26 09:53:23 2008 Succeeded!
Fri Dec 26 09:53:23 2008 Trying to find symbols for module (6 / 7) /lib64/tls/libc.so.6
Fri Dec 26 09:53:23 2008 Succeeded!
Fri Dec 26 09:53:23 2008 Trying to find symbols for module (7 / 7) /usr/lib64/libstdc++.so.6
Fri Dec 26 09:53:23 2008 Succeeded!
Fri Dec 26 09:53:23 2008 Done.
The Activity has finished running.

[xxx@n197 bin]$ /home/user/intel-vtune-9.1/vtune/bin/vtl show
VTune Performance Analyzer 9.1 for Linux*. 30 DAY EVALUATION LICENSE build 152
Copyright (C) 2000-2008 Intel Corporation. All rights reserved.

a1__autodock
r1___Call Graph Results [127.0.0.1] - Fri Dec 26 09:53:22 2008
---

and check now the sequence -

[xxx@n197 bin]$ /home/user/intel-vtune-9.1/vtune/bin/vtl activity autodock4 -c callgraph -app ./autodock4,10 -moi ./autodock4 run
VTune Performance Analyzer 9.1 for Linux*. 30 DAY EVALUATION LICENSE build 152
Copyright (C) 2000-2008 Intel Corporation. All rights reserved.

The Activity has been successfully created.
The Activity is running.
Fri Dec 26 09:56:58 2008 Reading property files started...

Fri Dec 26 09:56:58 2008 Reading property files done.

Fri Dec 26 09:56:59 2008 Static instrumentation started
Fri Dec 26 09:56:59 2008 All functions instrumentation of module "autodock4" was skipped.
Fri Dec 26 09:56:59 2008 Exports instrumentation of module "libc-2.3.4.so" was skipped.
Fri Dec 26 09:56:59 2008 Minimal instrumentation of module "libdl-2.3.4.so" was skipped.
Fri Dec 26 09:56:59 2008 Exports instrumentation of module "libgcc_s-3.4.6-20060404.so.1" was skipped.
Fri Dec 26 09:56:59 2008 All functions instrumentation of module "libimf.so" was skipped.
Fri Dec 26 09:56:59 2008 All functions instrumentation of module "libm-2.3.4.so" was skipped.
Fri Dec 26 09:56:59 2008 Exports instrumentation of module "libstdc++.so.6.0.3" was skipped.
Fri Dec 26 09:56:59 2008 Static instrumentation done
Fri Dec 26 09:56:59 2008 Data collection started...
Fri Dec 26 09:57:31 2008 Process Call Graph (MT) Data Collection, id "12036", started writing Call Graph data.

Fri Dec 26 09:57:31 2008 Process Call Graph (MT) Data Collection, id "12036", finished writing Call Graph data.

Fri Dec 26 09:57:31 2008 Copying results from remote machine...
Fri Dec 26 09:57:41 2008 Data collection finished...
Fri Dec 26 09:57:42 2008 Updating Call graph database...
Fri Dec 26 09:57:42 2008 Trying to find symbols for module (1 / 7) /home/mukesh/autodock-intel-compl/prefix/bin/autodock4
Fri Dec 26 09:57:42 2008 Succeeded!
Fri Dec 26 09:57:42 2008 Trying to find symbols for module (2 / 7) /apps/intel/cce/11.0.074/lib/intel64/libimf.so
Fri Dec 26 09:57:42 2008 Succeeded!
Fri Dec 26 09:57:42 2008 Trying to find symbols for module (3 / 7) /lib64/libgcc_s.so.1
Fri Dec 26 09:57:42 2008 Succeeded!
Fri Dec 26 09:57:42 2008 Trying to find symbols for module (4 / 7) /lib64/libdl.so.2
Fri Dec 26 09:57:42 2008 Succeeded!
Fri Dec 26 09:57:42 2008 Trying to find symbols for module (5 / 7) /lib64/ld-2.3.4.so
Fri Dec 26 09:57:42 2008 Succeeded!
Fri Dec 26 09:57:42 2008 Trying to find symbols for module (6 / 7) /lib64/tls/libc.so.6
Fri Dec 26 09:57:42 2008 Succeeded!
Fri Dec 26 09:57:42 2008 Trying to find symbols for module (7 / 7) /usr/lib64/libstdc++.so.6
Fri Dec 26 09:57:42 2008 Succeeded!
Fri Dec 26 09:57:42 2008 Done.
The Activity has finished running.

[xxx@n197 bin]$ /home/user/intel-vtune-9.1/vtune/bin/vtl show
VTune Performance Analyzer 9.1 for Linux*. 30 DAY EVALUATION LICENSE build 152
Copyright (C) 2000-2008 Intel Corporation. All rights reserved.

a1__autodock
r1___Call Graph Results [127.0.0.1] - Fri Dec 26 09:53:22 2008
a2__autodock4
r1___Call Graph Results [127.0.0.1] - Fri Dec 26 09:57:42 2008
---

Queries:

Why in first instance it does "All functions instrumentation of module "autodock4" was succesfull." but in second instance it shows a message of "All functions instrumentation of module "autodock4" was skipped."

While executing above command, I did perform "kill -12 PID (autodock_home)" after certain time could be 20-30 sec. I doubt this has any effects.

~BR

"Why in first instance it does"All functions instrumentation of module "autodock4" was succesfull."but in second instance it shows a message of"All functions instrumentation of module "autodock4" was skipped."

The reason is that call graph doesn't need to do instrumentation again at second time since your source / binaries haven't been changed.

Please use "vtl global-options" to know where your "cache-directory" (usually "/tmp/vtune_user/Cache" is. You can manually remove instrumented files, so next time call graph will instrument them again...

Happy new year!

Regards, Peter

Quoting - Zhen Yu Wang (Intel)

"Why in first instance it does "All functions instrumentation of module "autodock4" was succesfull." but in second instance it shows a message of "All functions instrumentation of module "autodock4" was skipped."

The reason is that call graph doesn't need to do instrumentation again at second time since your source / binaries haven't been changed.

Please use "vtl global-options" to know where your "cache-directory" (usually "/tmp/vtune_user/Cache" is. You can manually remove instrumented files, so next time call graph will instrument them again...

Happy new year!

Regards, Peter

Hi Peter.

Thanks for correcting.

I have few more queries as I am planning to perform both EBS & CallGraph analysis for Autodock4, -

(a) In VTune when we go for "First Use Wizard" option, we have to give the -
Application to launch:
Application arguements:
Working directory:

Can you suggest what options one has to pass as "Application arguements" or it should be empty. The reason of asking is - I am only getting disassembly part of code but not the source or source view?

(b) I can debug Autogrid4 using IDB or GDB with or w/o "--enable-debug=full" during it's configure script, but when I do the same for Autodock4, it says symbols not allocated or one can assume that Autodock4 failed to generate or have symbol table, any idea how to perform debugging for Autodock4 or what options should be passed so that one can have debugging sysmbols being generated for Autodock4 executable?

P.S: Autodock4 has been compiled using Intel C++ Compiler(v-11.0) and using Intel VTune(v-9.1) to perform profiling.

~BR

Quoting - srimks

Hi Peter.

Thanks for correcting.

I have few more queries as I am planning to perform both EBS & CallGraph analysis for Autodock4, -

(a) In VTune when we go for "First Use Wizard" option, we have to give the -
Application to launch:
Application arguements:
Working directory:

Can you suggest what options one has to pass as "Application arguements" or it should be empty. The reason of asking is - I am only getting disassembly part of code but not the source or source view?

(b) I can debug Autogrid4 using IDB or GDB with or w/o "--enable-debug=full" during it's configure script, but when I do the same for Autodock4, it says symbols not allocated or one can assume that Autodock4 failed to generate or have symbol table, any idea how to perform debugging for Autodock4 or what options should be passed so that one can have debugging sysmbols being generated for Autodock4 executable?

P.S: Autodock4 has been compiled using Intel C++ Compiler(v-11.0) and using Intel VTune(v-9.1) to perform profiling.

~BR

Hi,

a) Please use sampling wizard or call graph wizard.

Application to launch: autodock4_path/autodock4
Application augments: 100
Working directory: autodock4_path

These should be not source/assembly view relevant

b) You may discuss Intel C++ compiler and IDB issue on Intel C++ compiler forum.

Regards, Peter

Quoting - Zhen Yu Wang (Intel)

Quoting - srimks

Hi Peter.

Thanks for correcting.

I have few more queries as I am planning to perform both EBS & CallGraph analysis for Autodock4, -

(a) In VTune when we go for "First Use Wizard" option, we have to give the -
Application to launch:
Application arguements:
Working directory:

Can you suggest what options one has to pass as "Application arguements" or it should be empty. The reason of asking is - I am only getting disassembly part of code but not the source or source view?

(b) I can debug Autogrid4 using IDB or GDB with or w/o "--enable-debug=full" during it's configure script, but when I do the same for Autodock4, it says symbols not allocated or one can assume that Autodock4 failed to generate or have symbol table, any idea how to perform debugging for Autodock4 or what options should be passed so that one can have debugging sysmbols being generated for Autodock4 executable?

P.S: Autodock4 has been compiled using Intel C++ Compiler(v-11.0) and using Intel VTune(v-9.1) to perform profiling.

~BR

Hi,

a) Please use sampling wizard or call graph wizard.

Application to launch: autodock4_path/autodock4
Application augments: 100
Working directory: autodock4_path

These should be not source/assembly view relevant

b) You may discuss Intel C++ compiler and IDB issue on Intel C++ compiler forum.

Regards, Peter

Hi Peter,

I was able to get the debug information through IDB and source file information too using VTune with "First Use Wizard".

Probably, there were some issues with configure script of Autodock4 which didn't had option of of "-g" being generated for "config.status" file for CXXFLAGS after running the "./configure" script command.

TX.

~BR

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