From 75c31d2c5cd47eba2f19049c74f623a165ac81eb Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 18 Jul 2011 15:22:14 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6538 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_start.html | 78 +++++++++++++++++++++--------------------- doc/Section_start.txt | 78 +++++++++++++++++++++--------------------- 2 files changed, 78 insertions(+), 78 deletions(-) diff --git a/doc/Section_start.html b/doc/Section_start.html index d6f33a59d7..8977275e3c 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -341,6 +341,45 @@ Obj_name where it stores the system-specific *.o files. files created when LAMMPS is built, for either all builds or for a particular machine.

+

(3) Changing the size limits in src/lmptype.h +

+

If you are running a very large problem (billions of atoms or more) +and get a run-time error about the system being too big, either on a +per-processor basis or in total size, then you may need to change one +or more settings in src/lmptype.h and re-compile LAMMPS. +

+

As the documentation in that file explains, you have basically +two choices to make: +

+ +

The default for atom IDs is 4-byte integers since there is a memory +and communication cost for 8-byte integers. Non-molecular problems do +not need atom IDs so this does not restrict their size. Molecular +problems (which use IDs to define molecular topology), are limited to +about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they +are effectively unlimited in size (2^63). +

+

The default for total system size quantities (like the number of atoms +or timesteps) is 8-byte integers by default which is effectively +unlimited in size (2^63). If your system or MPI implementation does +not support 8-byte integers, an error will be generated, and you will +need to set "bigint" to 4-byte integers. This restricts your total +system size to about 2 billion atoms or timesteps (2^31). +

+

Note that in src/lmptype.h there are also settings for the MPI data +types associated with the integers that store atom IDs and total +system sizes, which need to be set consistent with the associated C +data types. +

+

In all cases, the size of problem that can be run on a per-processor +basis is limited by 4-byte integer storage to about 2 billion atoms +per processor (2^31), which should not normally be a restriction since +such a problem would have a huge per-processor memory footprint due to +neighbor lists and would run very slowly in terms of CPU +secs/timestep. +

Building for a Mac: @@ -377,45 +416,6 @@ third includes all standard packages (with the exceptions) and some user packages. The included user packages are USER-EFF, USER-CG-CMM, and USER-REAXC. The fourth project includes the USER-AWPMD package.

-

(5) Changing the size limits in src/lmptype.h -

-

If you are running a very large problem (billions of atoms or more) -and get a run-time error about the system being too big, either on a -per-processor basis or in total size, then you may need to change one -or more settings in src/lmptype.h and re-compile LAMMPS. -

-

As the documentation in that file explains, you have basically -two choices to make: -

- -

The default for atom IDs is 4-byte integers since there is a memory -and communication cost for 8-byte integers. Non-molecular problems do -not need atom IDs so this does not restrict their size. Molecular -problems (which use IDs to define molecular topology), are limited to -about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they -are effectively unlimited in size (2^63). -

-

The default for total system size quantities (like the number of atoms -or timesteps) is 8-byte integers by default which is effectively -unlimited in size (2^63). If your system does not support 8-byte -integers, an error will be generated, and you will need to set -"bigint" to 4-byte integers. This restricts your total system size to -about 2 billion atoms or timesteps (2^31). -

-

Note that in src/lmptype.h there are also settings for the MPI data -types associated with the integers that store atom IDs and total -system sizes, which need to be set consistent with the associated C -data types. -

-

In all cases, the size of problem that can be run on a per-processor -basis is limited by 4-byte integer storage to about 2 billion atoms -per processor (2^31), which should not normally be a restriction since -such a problem would have a huge per-processor memory footprint due to -neighbor lists and would run very slowly in terms of CPU -secs/timestep. -

2.3 Making LAMMPS with optional packages diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 0d91f1fd97..303366ec84 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -336,6 +336,45 @@ Typing "make clean-all" or "make clean-foo" will delete *.o object files created when LAMMPS is built, for either all builds or for a particular machine. +(3) Changing the size limits in src/lmptype.h + +If you are running a very large problem (billions of atoms or more) +and get a run-time error about the system being too big, either on a +per-processor basis or in total size, then you may need to change one +or more settings in src/lmptype.h and re-compile LAMMPS. + +As the documentation in that file explains, you have basically +two choices to make: + +set the data type size of integer atom IDs to 4 or 8 bytes +set the data type size of integers that store the total system size to 4 or 8 bytes :ul + +The default for atom IDs is 4-byte integers since there is a memory +and communication cost for 8-byte integers. Non-molecular problems do +not need atom IDs so this does not restrict their size. Molecular +problems (which use IDs to define molecular topology), are limited to +about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they +are effectively unlimited in size (2^63). + +The default for total system size quantities (like the number of atoms +or timesteps) is 8-byte integers by default which is effectively +unlimited in size (2^63). If your system or MPI implementation does +not support 8-byte integers, an error will be generated, and you will +need to set "bigint" to 4-byte integers. This restricts your total +system size to about 2 billion atoms or timesteps (2^31). + +Note that in src/lmptype.h there are also settings for the MPI data +types associated with the integers that store atom IDs and total +system sizes, which need to be set consistent with the associated C +data types. + +In all cases, the size of problem that can be run on a per-processor +basis is limited by 4-byte integer storage to about 2 billion atoms +per processor (2^31), which should not normally be a restriction since +such a problem would have a huge per-processor memory footprint due to +neighbor lists and would run very slowly in terms of CPU +secs/timestep. + :line [{Building for a Mac:}] :link(2_2_6) @@ -372,45 +411,6 @@ third includes all standard packages (with the exceptions) and some user packages. The included user packages are USER-EFF, USER-CG-CMM, and USER-REAXC. The fourth project includes the USER-AWPMD package. -(5) Changing the size limits in src/lmptype.h - -If you are running a very large problem (billions of atoms or more) -and get a run-time error about the system being too big, either on a -per-processor basis or in total size, then you may need to change one -or more settings in src/lmptype.h and re-compile LAMMPS. - -As the documentation in that file explains, you have basically -two choices to make: - -set the data type size of integer atom IDs to 4 or 8 bytes -set the data type size of integers that store the total system size to 4 or 8 bytes :ul - -The default for atom IDs is 4-byte integers since there is a memory -and communication cost for 8-byte integers. Non-molecular problems do -not need atom IDs so this does not restrict their size. Molecular -problems (which use IDs to define molecular topology), are limited to -about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they -are effectively unlimited in size (2^63). - -The default for total system size quantities (like the number of atoms -or timesteps) is 8-byte integers by default which is effectively -unlimited in size (2^63). If your system does not support 8-byte -integers, an error will be generated, and you will need to set -"bigint" to 4-byte integers. This restricts your total system size to -about 2 billion atoms or timesteps (2^31). - -Note that in src/lmptype.h there are also settings for the MPI data -types associated with the integers that store atom IDs and total -system sizes, which need to be set consistent with the associated C -data types. - -In all cases, the size of problem that can be run on a per-processor -basis is limited by 4-byte integer storage to about 2 billion atoms -per processor (2^31), which should not normally be a restriction since -such a problem would have a huge per-processor memory footprint due to -neighbor lists and would run very slowly in terms of CPU -secs/timestep. - :line 2.3 Making LAMMPS with optional packages :h4,link(2_3)