We are consistently receiving the following error:
munmap_chunk(): invalid pointer
leading to
.../linclust/sh: line 76: 2444 Aborted (core dumped) $RUNNER "$MMSEQS" "${ALIGN_MODULE}" "$INPUT" "$INPUT" "$RESULTDB" "${TMP_PATH}/aln" ${ALIGNMENT_PAR}
leading to:
"Error: Alignment step died"
"Error: Search died"
Steps to Reproduce (for bugs)
file used: seqs.fasta (download seqs.txt from this issue, then change the file name extension to .fasta)
command used: mmseqs easy-linclust seqs.fasta /tmp/mmseqs /tmp --min-seq-id 0.9 -c 1.0 --cov-mode 0
MMseqs Output (for bugs)
see screenshot
Your Environment
Include as many relevant details about the environment you experienced the bug in.
Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters): 13.4511 (see screenshot)
Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): Bioconda
For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: /
Server specifications (especially CPU support for AVX2/SSE and amount of system memory): support for both AVX2 and SSE
Operating system and version: centos 8, 48 CPU, 192 GB RAM, 512 GB disk memory (m5.12xlarge instance AWS)
This is a small bug in the release, which only occurs with sequences smaller than alphabet size, it is already fixed in the current github version. The relevant commit is c7f6a37
Current Behavior
We are consistently receiving the following error: munmap_chunk(): invalid pointer leading to .../linclust/sh: line 76: 2444 Aborted (core dumped) $RUNNER "$MMSEQS" "${ALIGN_MODULE}" "$INPUT" "$INPUT" "$RESULTDB" "${TMP_PATH}/aln" ${ALIGNMENT_PAR} leading to: "Error: Alignment step died" "Error: Search died"
Steps to Reproduce (for bugs)
file used: seqs.fasta (download seqs.txt from this issue, then change the file name extension to .fasta) command used: mmseqs easy-linclust seqs.fasta /tmp/mmseqs /tmp --min-seq-id 0.9 -c 1.0 --cov-mode 0
MMseqs Output (for bugs)
see screenshot
Your Environment
Include as many relevant details about the environment you experienced the bug in.
seqs.txt
Please let us know if there is anything else you need. Thanks in advance!