segfault doing string operations possibly related to TBB

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1

I’m getting a segfault when creating a string variable of other string variables specifically when using an Intel compiler and the USER-INTEL package. I’ve tracked it down to including libtbbmalloc in the supplied Intel Makefiles, that is, if I remove -ltbbmalloc and add -DLMP_INTEL_NO_TBB to CCFLAGS, the problem goes away. Also, if I compile without the USER-INTEL package, the problem goes away.

The problem comes when I make a new string variable that contains 2 (or more) string variables, which itself is not a problem, but if I try to make this new string part of another string variable, I get the segfault. Here is a basic script that reproduces the problem for me:

variable a string 10

variable b string 300

variable id string “a-{a}-b-{b}”

variable some_directory string “data/${id}” # <-- causes the segfault

The error that gets printed starts with: “*** glibc detected *** ./lmp_intel_cpu: free(): invalid pointer…” Then a backtrace that points to /lib64/libc.so.6. I would copy more of the error message but I’m working on an air-gapped cluster and would have to type it all out by hand. Let me know if there’s something specific you want to see.

I’ve tried a couple different machines with Intel 17.0.1 and 18.0.3 compilers and can reliably reproduce the error on the different configurations. Unfortunately I cannot change the way these compilers were built in case it is a system configuration issue.

I realize I have a couple of outs here: just use pure MPI and don’t worry about threads, or don’t use an intermediate string variable - but I’m just trying to understand the root of this problem. Any ideas?

Thanks.

  • Jesse
2

which LAMMPS version?

3

Latest stable (June 2019).

4

ok. been doing a little test with valgrind’s memory checker. it looks there is a mismatch of using malloc()/free() with new/delete. the use of TBB may just make it more visible.

please try with the following modification:

$ git show
commit 3e2f3a80583494420eda14e4ce178f5b71695e60 (HEAD -> collected-small-fixes, devel/collected-small-fixes)
gpg: Signature made Mon 10 Jun 2019 06:22:04 PM EDT
gpg: using RSA key EEA103764C6C633EDC8AC428D9B44E93BF0C375A
gpg: Good signature from “Axel Kohlmeyer <[email protected]>” [ultimate]
Author: Axel Kohlmeyer <[email protected]…24…>

avoid a case of mixing malloc()/free() with new/delete

diff --git a/src/variable.cpp b/src/variable.cpp
index 376cc8045…7cbdc57d3 100644
— a/src/variable.cpp
+++ b/src/variable.cpp
@@ -288,11 +288,11 @@ void Variable::set(int narg, char **arg)

int maxcopy = strlen(arg[2]) + 1;
int maxwork = maxcopy;

  • char *scopy = new char[maxcopy];
  • char *work = new char[maxwork];
  • char *scopy = (char *) memory->smalloc(maxcopy,“var:string/copy”);
  • char *work = (char *) memory->smalloc(maxwork,“var:string/work”);
    strcpy(scopy,arg[2]);
    input->substitute(scopy,work,maxcopy,maxwork,1);
  • delete [] work;
  • memory->sfree(work);

int ivar = find(arg[0]);
if (ivar >= 0) {
@@ -310,7 +310,7 @@ void Variable::set(int narg, char *arg)
data[nvar] = new char[num[nvar]];
copy(1,&scopy,data[nvar]);
}

  • delete [] scopy;
  • memory->sfree(scopy);

// GETENV
// remove pre-existing var if also style GETENV (allows it to be reset)

5

That patch appears to have worked! Thanks!

6

thanks for the feedback. the change will be included in the next LAMMPS patch release. axel.