helgrind doesn't see/know about the glibc internal locking done for FILE *state and so suppresses any races in glibc itself. From glibc-2.34567-NPTL-helgrind.supp:

# - suppress anything that has its top frame in libc.so.
#   This really isn't clever, since it could hide some 
#   legitimate races.  But the problem is, if we don't do
#   this, then loads of errors to do with stdio are reported, because
#   H fails to see glibc's internal locking/unlocking of FILE*s
#   as required by POSIX.  A better solution is needed.

{
   helgrind-glibc2X-004
   Helgrind:Race
   obj:*/lib*/libc-2.*so*
}

Newer glibc might use mempcpy to manipulate FILE* state since:

2012-03-29  David S. Miller  <davem@davemloft.net>

       * libio/fileops.c (_IO_new_file_xsputn): Don't try to optimize
       small copies by hand.

The code now just uses mempcpy to do the copying.

This causes a simple program like:

#include <stdio.h>
#include <pthread.h>

pthread_t thread;

void* thread3 (void* d)
{
  int count3 = 0;

  while(count3 < 100){
    printf("Thread 3: %d\n", count3++);
  }
  return NULL;
}

void* thread2 (void* d)
{
  int count2 = 0;

  while(count2 < 1000){
	  //
    printf("Thread 2: %d\n", count2++);
  }
  return NULL;
}

int main (){

  pthread_create (&thread, NULL, thread2, NULL);
  pthread_create (&thread, NULL, thread3, NULL);

  //Thread 1
  int count1 = 0;

  while(count1 < 10){
    printf("Thread 1: %d\n", count1++);
  }

  pthread_join(thread,NULL);
  return 0;
}

$ gcc -g -o threads -lpthread threads.c
$ valgrind --tool=helgrind ./threads

To produce:

==6367== ----------------------------------------------------------------
==6367== 
==6367== Possible data race during write of size 1 at 0x4022009 by thread #1
==6367== Locks held: none
==6367==    at 0x4C3422C: __GI_mempcpy (in /usr/lib64/valgrind/vgpreload_helgrind-amd64-linux.so)
==6367==    by 0x50CF0E1: _IO_file_xsputn@@GLIBC_2.2.5 (fileops.c:1307)
==6367==    by 0x509F66F: vfprintf (vfprintf.c:1323)
==6367==    by 0x50A9E78: printf (printf.c:33)
==6367==    by 0x40077D: main (threads.c:36)
==6367==  Address 0x4022009 is not stack'd, malloc'd or on a free list
==6367== 
==6367== ----------------------------------------------------------------
==6367== 
==6367== Possible data race during write of size 1 at 0x402200A by thread #1
==6367== Locks held: none
==6367==    at 0x4C34249: __GI_mempcpy (in /usr/lib64/valgrind/vgpreload_helgrind-amd64-linux.so)
==6367==    by 0x50CF0E1: _IO_file_xsputn@@GLIBC_2.2.5 (fileops.c:1307)
==6367==    by 0x50A31EC: vfprintf (vfprintf.c:1641)
==6367==    by 0x50A9E78: printf (printf.c:33)
==6367==    by 0x40077D: main (threads.c:36)
==6367==  Address 0x402200a is not stack'd, malloc'd or on a free list
==6367== 
==6367== ----------------------------------------------------------------
==6367== 
==6367== Possible data race during write of size 1 at 0x402200B by thread #1
==6367== Locks held: none
==6367==    at 0x4C3422C: __GI_mempcpy (in /usr/lib64/valgrind/vgpreload_helgrind-amd64-linux.so)
==6367==    by 0x50CF0E1: _IO_file_xsputn@@GLIBC_2.2.5 (fileops.c:1307)
==6367==    by 0x50A2F0D: vfprintf (vfprintf.c:1673)
==6367==    by 0x50A9E78: printf (printf.c:33)
==6367==    by 0x40077D: main (threads.c:36)
==6367==  Address 0x402200b is not stack'd, malloc'd or on a free list
==6367== 


Reproducible: Always




Proposed patch:

diff --git a/glibc-2.34567-NPTL-helgrind.supp b/glibc-2.34567-NPTL-helgrind.supp
index b61a339..ed105b8 100644
--- a/glibc-2.34567-NPTL-helgrind.supp
+++ b/glibc-2.34567-NPTL-helgrind.supp
@@ -23,6 +23,10 @@
 #   this, then loads of errors to do with stdio are reported, because
 #   H fails to see glibc's internal locking/unlocking of FILE*s
 #   as required by POSIX.  A better solution is needed.
+#
+# - some of the stdio functions in newer glibc manipulate stdio
+#   FILE*s state through mempcpy, which we intercept, so we also need
+#   to suppress such manipulations.
 
 #{
 #   helgrind-glibc2X-001
@@ -41,6 +45,14 @@
 }
 
 {
+   helgrind-glibc-io-xsputn-mempcpy
+   Helgrind:Race
+   fun:__GI_mempcpy
+   fun:_IO_*xsputn*
+   obj:*/lib*/libc-2.*so*
+}
+
+{
    helgrind-glibc2X-005
    Helgrind:Race
    obj:*/lib*/libpthread-2.*so*