Dear all,
I attempted to run a simple simulation involving diffusion of a coarse-grained polymer in a LB fluid using a single MPI process. Please find attached the input script and data files used, which are called test.in and test.dat respectively. At the end of the run, I received the following messages appended to the usual LAMMPS output:
In direct memory block for handle type DATATYPE, 3 handles are still allocated
In indirect memory block 0 for handle type DATATYPE, 17 handles are still allocated
I have run the code through valgrind and the output can be found in the attached file named ‘ct.23397’. The problem appears to lie with the routines used to read the input script and/or data file in the Input class.
The details of the hardware and software used are as follows:
LAMMPS version : 5June19
Hardware: Intel® Xeon® CPU X5650 @ 2.67GHz
OS : CentOS release 6.9
Compiler: mpicxx
MPI Library: mvapich2-1.9
I tried to log an issue on GitHub but it wouldn’t accept the file format of the attachments. May I know where the issue lies?
Best,
Karthik
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ct.23397 (9.39 KB)
test.dat (6.11 KB)
test.in (709 Bytes)
Dear all,
I attempted to run a simple simulation involving diffusion of a coarse-grained polymer in a LB fluid using a single MPI process. Please find attached the input script and data files used, which are called test.in and test.dat respectively. At the end of the run, I received the following messages appended to the usual LAMMPS output:
In direct memory block for handle type DATATYPE, 3 handles are still allocated
In indirect memory block 0 for handle type DATATYPE, 17 handles are still allocated
these are not messages from LAMMPS, but it looks like they are generated by your MPI library. they also seem to be warnings and not errors.
I have run the code through valgrind and the output can be found in the attached file named ‘ct.23397’. The problem appears to lie with the routines used to read the input script and/or data file in the Input class.
that is not correct. all issues indicated by valgrind seem to be due to MPI library calls and and specifically related to accessing the infiniband device. they are triggered when LAMMPS exits normally. this is definitely not a LAMMPS issue.
The details of the hardware and software used are as follows:
LAMMPS version : 5June19
Hardware: Intel® Xeon® CPU X5650 @ 2.67GHz
OS : CentOS release 6.9
Compiler: mpicxx
MPI Library: mvapich2-1.9
I tried to log an issue on GitHub but it wouldn’t accept the file format of the attachments. May I know where the issue lies?
github will accept those files, if you change the names to end in .txt.
axel.