Re: Error message 'std::bad_alloc'
Francesco Pietra 15:29 Wed 16 Apr The std:: would to me make me think C++ namespace 'std' function 'bad_alloc'. So probably a bad_alloc function exists in C++ and is returning an error. It is a standard exception thrown when the new() operator fails. Your running out of RAM, perhaps. Do you build this program yourself from source? Yes (g77-3.4 g++ 4.1.2 lib2c0-dev) from the configure file provided by developers. No errors in either the serial or parallel compilations (openmpi). Also, there is a very long test for both the serial and parallel execution. All passed with a few marginal warnings for different precision on different machines. Finally, docking of a slightly smaller ligands occurs with no errors. I'd build with debug info and run it under gdb and/or valgrind. Might tell you where it is messing up. -- I develop for Linux for a living, I used to develop for DOS. Going from DOS to Linux is like trading a glider for an F117. (By [EMAIL PROTECTED], Lawrence Foard) -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Error message 'std::bad_alloc'
Hi: OK. However, as my experience with compilations is very limited, could you give a web indication where to learn how to build with debug info and run it under gdb and/or valgrind. Meanwhile I am starting a molecular dynamics simulation. As soon as completed (1-3 days, have not yet checked the speed of the new machine) I'll follow your indications. Thanks francesco pietra --- On Thu, 4/17/08, C. Ahlstrom [EMAIL PROTECTED] wrote: From: C. Ahlstrom [EMAIL PROTECTED] Subject: Re: Error message 'std::bad_alloc' To: Francesco Pietra [EMAIL PROTECTED] Cc: Lennart Sorensen [EMAIL PROTECTED], debian64 debian-amd64@lists.debian.org Date: Thursday, April 17, 2008, 4:02 AM Francesco Pietra 15:29 Wed 16 Apr The std:: would to me make me think C++ namespace 'std' function 'bad_alloc'. So probably a bad_alloc function exists in C++ and is returning an error. It is a standard exception thrown when the new() operator fails. Your running out of RAM, perhaps. Do you build this program yourself from source? Yes (g77-3.4 g++ 4.1.2 lib2c0-dev) from the configure file provided by developers. No errors in either the serial or parallel compilations (openmpi). Also, there is a very long test for both the serial and parallel execution. All passed with a few marginal warnings for different precision on different machines. Finally, docking of a slightly smaller ligands occurs with no errors. I'd build with debug info and run it under gdb and/or valgrind. Might tell you where it is messing up. -- I develop for Linux for a living, I used to develop for DOS. Going from DOS to Linux is like trading a glider for an F117. (By [EMAIL PROTECTED], Lawrence Foard) -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Error message 'std::bad_alloc'
On Thursday 17 April 2008 16.09.38 Francesco Pietra wrote: Hi: OK. However, as my experience with compilations is very limited, could you give a web indication where to learn how to build with debug info and run it under gdb and/or valgrind. Meanwhile I am starting a molecular dynamics simulation. As soon as completed (1-3 days, have not yet checked the speed of the new machine) I'll follow your indications. Thanks francesco pietra Hi Francesco, Run the compiler (g++) with the -g flag to add debug info (configure the source using 'CXXFLAGS=-g ./configure' should do the trick). You can debug the application by running gdb as 'gdb --args prog args'. When it dies, type bt to dump the callstack. // Anders --- On Thu, 4/17/08, C. Ahlstrom [EMAIL PROTECTED] wrote: From: C. Ahlstrom [EMAIL PROTECTED] Subject: Re: Error message 'std::bad_alloc' To: Francesco Pietra [EMAIL PROTECTED] Cc: Lennart Sorensen [EMAIL PROTECTED], debian64 debian-amd64@lists.debian.org Date: Thursday, April 17, 2008, 4:02 AM Francesco Pietra 15:29 Wed 16 Apr The std:: would to me make me think C++ namespace 'std' function 'bad_alloc'. So probably a bad_alloc function exists in C++ and is returning an error. It is a standard exception thrown when the new() operator fails. Your running out of RAM, perhaps. Do you build this program yourself from source? Yes (g77-3.4 g++ 4.1.2 lib2c0-dev) from the configure file provided by developers. No errors in either the serial or parallel compilations (openmpi). Also, there is a very long test for both the serial and parallel execution. All passed with a few marginal warnings for different precision on different machines. Finally, docking of a slightly smaller ligands occurs with no errors. I'd build with debug info and run it under gdb and/or valgrind. Might tell you where it is messing up. -- I develop for Linux for a living, I used to develop for DOS. Going from DOS to Linux is like trading a glider for an F117. (By [EMAIL PROTECTED], Lawrence Foard) -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] ___ _ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Error message 'std::bad_alloc'
I am looking for the meaning of the following error message: terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc Aborted which occurs on running a chemical computational program (serial run) on a eighth logical 875 opterons system with 24GB RAM (all activated with shmmax and also setting the stack size to 'unlimited'), Debian amd64 etch. The maintainers of the computational program wrote: A little gooogggling of debian std::bad_alloc didn't find much. Naturally you should verify that all the debian/glib/gcc patches have been applied. The computational program was gcc compiled on my previous system with four logical 265 opterons and 16GB RAM and I am using the same raid1 HDD with the new system, where of course I have reset shmmax. The simulation concerns docking a molecule onto a protein. When the molecule is slightly smaller, no error message occurs and the procedure ends correctly; therefore I don't understand why the maintainer allude to a possible lack of patches. The same events occurred on the 265 system mentioned above, and the maintainers thought there was not enough RAM. For intrinsic reasons of the molecular system treated, the procedure can't be run parallel; in any case I should launch mpirun -np 1 (not 8) ... Thanks francesco pietra Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Error message 'std::bad_alloc'
On Wed, Apr 16, 2008 at 10:04:56AM -0700, Francesco Pietra wrote: I am looking for the meaning of the following error message: terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc Aborted which occurs on running a chemical computational program (serial run) on a eighth logical 875 opterons system with 24GB RAM (all activated with shmmax and also setting the stack size to 'unlimited'), Debian amd64 etch. The maintainers of the computational program wrote: A little gooogggling of debian std::bad_alloc didn't find much. Naturally you should verify that all the debian/glib/gcc patches have been applied. The computational program was gcc compiled on my previous system with four logical 265 opterons and 16GB RAM and I am using the same raid1 HDD with the new system, where of course I have reset shmmax. The simulation concerns docking a molecule onto a protein. When the molecule is slightly smaller, no error message occurs and the procedure ends correctly; therefore I don't understand why the maintainer allude to a possible lack of patches. The same events occurred on the 265 system mentioned above, and the maintainers thought there was not enough RAM. For intrinsic reasons of the molecular system treated, the procedure can't be run parallel; in any case I should launch mpirun -np 1 (not 8) ... The std:: would to me make me think C++ namespace 'std' function 'bad_alloc'. So probably a bad_alloc function exists in C++ and is returning an error. I personally try to avoid dealing with C++ code anymore. It is getting too ugly after the STL stuff went in. Try a search for 'C++ bad_alloc' and you will find lots of stuff on bad_alloc in the C++ std library. About 45000 hits in google. -- Len Sorensen -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Error message 'std::bad_alloc'
Lennart Sorensen 14:49 Wed 16 Apr On Wed, Apr 16, 2008 at 10:04:56AM -0700, Francesco Pietra wrote: terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc which occurs on running a chemical computational program (serial run) on a eighth logical 875 opterons system with 24GB RAM (all activated with shmmax and also setting the stack size to 'unlimited'), Debian amd64 etch. The std:: would to me make me think C++ namespace 'std' function 'bad_alloc'. So probably a bad_alloc function exists in C++ and is returning an error. It is a standard exception thrown when the new() operator fails. Your running out of RAM, perhaps. Do you build this program yourself from source? I personally try to avoid dealing with C++ code anymore. It is getting too ugly after the STL stuff went in. Nahhh, the STL is great stuff! -- Only two kinds of witnesses exist. The first live in a neighborhood where a crime has been committed and in no circumstances have ever seen anything or even heard a shot. The second category are the neighbors of anyone who happens to be accused of the crime. These have always looked out of their windows when the shot was fired, and have noticed the accused person standing peacefully on his balcony a few yards away. -- Sicilian police officer -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Error message 'std::bad_alloc'
Hi: --- On Wed, 4/16/08, C. Ahlstrom [EMAIL PROTECTED] wrote: From: C. Ahlstrom [EMAIL PROTECTED] Subject: Re: Error message 'std::bad_alloc' To: Lennart Sorensen [EMAIL PROTECTED] Cc: Francesco Pietra [EMAIL PROTECTED], debian64 debian-amd64@lists.debian.org Date: Wednesday, April 16, 2008, 2:49 PM Lennart Sorensen 14:49 Wed 16 Apr On Wed, Apr 16, 2008 at 10:04:56AM -0700, Francesco Pietra wrote: terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc which occurs on running a chemical computational program (serial run) on a eighth logical 875 opterons system with 24GB RAM (all activated with shmmax and also setting the stack size to 'unlimited'), Debian amd64 etch. The std:: would to me make me think C++ namespace 'std' function 'bad_alloc'. So probably a bad_alloc function exists in C++ and is returning an error. It is a standard exception thrown when the new() operator fails. Your running out of RAM, perhaps. Do you build this program yourself from source? Yes (g77-3.4 g++ 4.1.2 lib2c0-dev) from the configure file provided by developers. No errors in either the serial or parallel compilations (openmpi). Also, there is a very long test for both the serial and parallel execution. All passed with a few marginal warnings for different precision on different machines. Finally, docking of a slightly smaller ligands occurs with no errors. francesco I personally try to avoid dealing with C++ code anymore. It is getting too ugly after the STL stuff went in. Nahhh, the STL is great stuff! -- Only two kinds of witnesses exist. The first live in a neighborhood where a crime has been committed and in no circumstances have ever seen anything or even heard a shot. The second category are the neighbors of anyone who happens to be accused of the crime. These have always looked out of their windows when the shot was fired, and have noticed the accused person standing peacefully on his balcony a few yards away. -- Sicilian police officer -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
