PC specification for Mascot Server
Introduction
Mascot Server uses a client-server architecture, where a client program feeds data to the server and downloads the results. Common configurations are:
- Mascot Server runs on PC 1 and Mascot Distiller runs on PC 2.
- Mascot Server runs on PC 1 and an instrument data system (e.g. Thermo Proteome Discoverer™) runs on PC 2.
- Mascot Server and Mascot Distiller run on the same PC.
In case #1, check PC specification for Mascot Distiller for PC 2. The rest of this document provides recommendations for PC 1.
In case #2, you should consult the third-party application’s requirements. The rest of this document provides recommendations for PC 1.
In case #3, you will need more RAM on the one PC and you may need a more powerful processor. These are noted below where appropriate.
Quick reference
Any recent, high specification PC containing either Intel or AMD Ryzen processor(s) should make a suitable platform for Mascot. A GPU is not required.
Mascot Server is licensed in three tiers: Small (8 cores), Medium (16 cores) and Large (up to 128 cores).
For running DIA searches, we recommend a Medium licence with 16-24 processor cores, with high ‘turbo’ clock speed (at least 4 GHz), at least 32GB of RAM and the largest SSD or NVMe disks available (at least 2TB).
For running DDA searches, a Small licence is sufficient, with 8-16 processor cores.
It is beneficial to put the operating system, Mascot program files and database search results on a solid state NVMe disk. Sequence databases can be stored on a bulk SSD drive.
Hardware virtualisation is discussed in Hardware virtualisation.
Speed versus throughput
Speed and throughput are related but different goals. Speed refers to the duration taken to process a file, while throughput is the number of files processed in a unit of time (say files per hour).
You can increase database search speed by adding more CPU cores/threads to the PC. However, as you add more threads, processing can hit other limiting factors such as code synchronisation points, file and memory access. Exactly when the increase in performance tails off will depend on the CPU type, workload and type of data.
For increasing speed, the Large licence (up to 128 cores) is beneficial for searching very large sequence databases, large number of variable modifications, no-enzyme searches and error tolerant searches. We recommend a dual processor system (e.g. 2×32 or 2×64 cores), as these have better speed than a single processor with 128 cores.
Increasing throughput requires a system-level perspective. In Mascot DIA and Mascot DDA, processing is split between Mascot Server and Mascot Distiller. To increase throughput on server side, you can run multiple searches concurrently. Mascot Server has a default soft limit of 10 concurrent searches. For example, if you have a Medium licence (16 cores) and the processor has 32 cores, then running 2-3 searches concurrently will maximise resource usage. Any number of client applications, like Mascot Distiller, can submit searches to the same Mascot server. Check the Mascot Distiller PC specification for how to increase client-side throughput.
Processor (CPU)
The two main PC processor manufacturers are Intel and AMD. Matrix Science does not currently support Mascot Server on other processor architectures.
Processor speed
The main factors affecting Mascot performance are processor clock speed and number of cores.
It is not possible to compare processor speeds directly for different architectures. However, for any given processor model, the search speed will be proportional to processor speed unless:
- Disk access becomes a bottleneck, for example if the FASTA sequence database has to be read into memory from disk (see section on RAM below) or
- The processor cache is too small and causes a bottleneck between processor and memory.
The PassMark CPU benchmark is a pretty good guide as to the performance you can expect for Mascot searches. The important benchmark for processor speed is single thread performance, because the cost of a Mascot Server licence depends on the number of cores used for searches.
If you are running Mascot Distiller on the same PC, we recommend AMD Threadripper or AMD EPYC. These processors have both excellent single-thread performance and excellent multi-threaded performance.
Number of cores
Mascot Server is licensed in three tiers: Small (8 cores), Medium (16 cores) and Large (128 cores). Most PCs have one processor socket, but workstations and server-grade system boards may have two or more sockets.
We have observed excellent scalability for systems with modest numbers of cores per processor. That is, throughput from a system with a 16 core processor can be very close to double that obtained from a processor with 8 cores and the same architecture and clock speed. However, power management for processors with large numbers of cores means that the clock frequency is progressively reduced as the workload increases, which causes scaling to become non-linear.
For licensing purposes, it does not matter how the cores are divided among the processors.
- 1 x 8-core processor requires a Small Mascot licence
- 1 x 12-core processor requires a Small mascot licence (leaving 4 cores for overheads)
- 1 x 16-core processor requires a Medium Mascot licence
- 2 x 12-core processors requires a Medium Mascot licence (leaving 8 cores for overheads)
It is always wise to have a few spare cores for running reports, or downloading and preparing databases.
If you are running Mascot Distiller on the same PC, check Mascot Distiller requirements. For Small or Medium licence, we recommend getting a processor with double the number of cores.
Intel Hybrid Architectures
Recent Intel processor families for desktop and mobile have a hybrid core architecture, starting from the 12th generation Intel Core processors. For example, Intel Core i7 12700 has 8 ‘ P’ performance and 4 ‘E’ efficiency cores.
Mascot Server can be run on both P and E cores, but do note that E cores are typically much slower than P cores. It is better to buy a processor with at least 8 P cores, preferably more. Alternatively, choose Intel Xeon or AMD processors which do not have this limitation.
64-bit
Mascot Server requires 64-bit processor architecture. All modern Intel and AMD processors are 64-bit or, in Intel terms, have “Intel EM64T” technology. All recent versions of Windows and Linux are fully 64-bit.
Hyper-Threading or Simultaneous Multithreading technology
Hyper-Threading is available on Intel processors. Recent AMD processors (Zen microarchitecture) have similar technology called Simultaneous Multithreading. Hyper-Threading works by duplicating certain sections of the processor – those that store the architectural state – but not duplicating the main execution resources. This allows a Hyper-Threading equipped processor to pretend to be two “logical” processors to the host operating system, allowing the operating system to schedule two threads or processes simultaneously.
When HT is enabled, 2 logical “processors” per core will be visible to Mascot Server. So, for example, a single physical Intel Xeon® Gold 5210 with 14 cores and HT will appear to have 28 logical processors. A single physical AMD Ryzen 9 5900X with 12 cores and Simultaneous Multithreading will appear to have 24 logical processors.
Hyper-threading can give up to a 12% performance increase.
For Mascot Server, hyper-threading does not count towards the number of cores used for licensing purposes. For example, a Medium licence (up to 16 cores) with Intel Xeon® Gold 5210 with 14 cores uses 14 physical cores (28 logical processors).
Random Access Memory (RAM)
RAM requirements for a Mascot database search depend on the selection of databases you plan to search as well as the number of simultaneous users of the Mascot Server system. Memory usage also depends on which task is being run, described below.
If you are running Mascot Distiller on the same PC, check Mascot Distiller requirements. It is best to allocate 32GB to Mascot Server and 32GB to Mascot Distiller, for a total of 64GB.
RAM usage during database compression
Mascot Monitor makes a compressed copy of each FASTA database, in which the title lines have been removed and the sequence strings have been packed in a byte efficient manner. The compressed copy of each database is mapped into RAM and, if there is sufficient room, can even be locked into memory.
RAM usage during database compression is negligible for most databases, because only small parts of the database are kept in memory at any given time.
The exception is NCBIprot. This database is extremely large (>700 million sequences as of January 2024) and may contain duplicate accession numbers. Mascot automatically detects duplicate accessions during database compression using an in-memory data structure. However, the size of the database means a lot of RAM is used for this purpose, up to 20GB.
If you intend to use NCBIprot, we recommend at least 32GB of RAM.
RAM usage during database search
Memory usage during a database search will fluctuate. Maximum memory usage can be estimated from the number of search threads. For each thread, you should allow approximately 60 MB for the operating system (Windows) and at least 200 MB for temporary storage. Thus, a search with 8 threads may use up to 2GB of RAM.
The actual memory usage depends on a number of factors, such as how many variable modifications are selected. A search with just 1 variable modification on a Small licence will peak at around 1000MB. The same search on a Medium licence will use 2x the amount of RAM.
Mascot Server allows up to 10 concurrent searches by default (this soft limit can be increased). If you have more than one user, you should multiply the above guideline with the anticipated maximum number of concurrent searches.
Memory mapping
When a search calls for a database that is not in memory, the search duration is increased by the time taken to read the database from disk. For a search that takes longer than a couple of minutes, this additional time will be negligible. For a short search, for example a PMF or an MS/MS search of a few spectra, reading from disk may take longer than the search itself.
Databases should always be memory mapped, even though a system might not have sufficient physical RAM to hold them all. Memory mapping only consumes virtual address space, and enables the file to be accessed more efficiently. However, it doesn’t guarantee that a particular database will be in memory when a search calls for it; some other process may have kicked it out. So, it may be advantageous to lock a small, frequently searched database into memory, guaranteeing that it is always resident in RAM.
Whether you have sufficient RAM to lock a database in memory can be estimated from the size of the FASTA file. For a protein database, the required RAM is roughly 80% of the FASTA file size, while for a nucleic acid database it is roughly 50%. Some examples are given in the following table.
| Database | FASTA | RAM | Compression |
|---|---|---|---|
| Swiss-Prot | 272 MB | 245 MB | 1 : 0.9 |
| NCBIprot | 339 GB | 271 GB | 1 : 0.8 |
| Plants_EST | 18 GB | 8.9 GB | 1 : 0.5 |
We do not recommend that very large databases like TrEMBL, NCBIprot or UniRef100 be locked into memory.
RAM usage during machine learning
Database search results can optionally be refined using machine learning. Refining takes place at the end of the database search. Mascot uses two third-party utilities for refining: MS2Rescore and Percolator.
Memory usage for MS2Rescore depends on the type of model being used. Predicting MS/MS fragmentation spectra using MS2PIP can use 500-1000MB per thread. Mascot allocates 4-32 threads for MS2Rescore depending on the number of logical cores on the system. Predicting retention times using DeepLC is multithreaded and may use up to 30GB of RAM. If your system has more than one Mascot user, multiply these figures by the number of concurrent users to get a worst-case scenario.
Memory usage for Percolator is negligible compared to the above factors.
RAM usage when viewing reports or exporting results
When you browse the results in a web browser or export to a file, relatively little memory is used compared to the above tasks.
Hard Disk Storage
The Mascot Server program files require little disk space in comparison to the sequence databases and the accumulating result files.
If you are running Mascot Distiller on the same PC, check Mascot Distiller requirements. You will need enough space for both.
Sequence databases
For the sequence databases, you will need to maintain free disk space of the order of 3 times the largest database. This is because, during a database update, there may be the current FASTA file, reference file and its associated compressed files plus the equivalent for the incoming database. Mascot also keeps a copy of one previous database. Example (July 2024) disk requirements for the common databases are:
| Database | Total size of files (GB) | Max disk space (GB) |
|---|---|---|
| Swiss-Prot | 4.3 | 13 |
| TrEMBL | 230 | 690 |
| NCBIprot | 670 | 2010 |
This illustrates how storage requirements are strongly dependent on which databases are required.
Result files
The space needed for result files depends on the overall search profile and on how long results are to remain on-line. Individual result file sizes range from 1MB for a peptide mass fingerprint search through to several GB for a large LC-MS/MS dataset.
Disk drives are very inexpensive, and most PCs support up to 2-3 NVMe drives and four SATA devices. It is difficult to have too much disk space, especially if you plan to search databases similar in size to NCBIprot.
If any databases are not memory mapped, short searches may be disk I/O bound, and a fast disk (e.g. NVMe) or a disk array (e.g. RAID) can become an important factor in maximising throughput.
Operating System
Microsoft Windows
The following versions of Windows are supported:
| Operating System | Max processor sockets | Max cores | Max RAM |
|---|---|---|---|
| Windows 10 Pro – 64 bit | 2 | 256 | 2 TB |
| Windows 10 Enterprise – 64 bit | 2 | 256 | 6 TB |
| 2016 Server Standard – 64 bit | 64 | unlimited | 24 TB |
| 2016 Server Datacenter – 64 bit | 64 | unlimited | 24 TB |
| 2019 Server Standard – 64 bit | 64 | unlimited | 24 TB |
| 2019 Server Datacenter – 64 bit | 64 | unlimited | 24 TB |
| 2022 Server Standard – 64 bit | 64 | unlimited | 256 TB |
| 2022 Server Datacenter – 64 bit | 64 | unlimited | 256 TB |
| 2025 Server Standard – 64 bit | 64 | unlimited | 256 TB |
| 2025 Server Datacenter – 64 bit | 64 | unlimited | 256 TB |
| Windows 11 Pro – 64 bit | 2 | 256 | 2 TB |
| Windows 11 Enterprise – 64 bit | 2 | 256 | 6 TB |
- Windows Server Core editions are not supported
- Windows Home Basic and Starter editions are not supported
- If you need to run Mascot on an earlier version of Windows, your licence allows running any earlier version of Mascot that supported the target Windows version
Linux
Mascot has very few system dependencies on Linux. The main requirement is glibc 2.17 or later, which is satisfied by most Linux distributions released since 2014. The table below lists the oldest supported versions for the major distributions.
| Distribution | Minimum version | Recommended version |
|---|---|---|
| CentOS | CentOS 7 (glibc 2.17) | RedHat Enterprise Linux, AlmaLinux or Rocky Linux (CentOS has been discontinued) |
| Debian | Debian 9 ‘stretch’ (glibc 2.24) | Any later version |
| Ubuntu | Ubuntu 16.04 LTS (glibc 2.23) | Any later version |
| Amazon | Amazon Linux 2 (glibc 2.26) | Any recent version |
Mascot is tested in-house on various versions of Debian, Ubuntu and CentOS.
Web Server Software
Mascot requires a web server for administration and interactive use. In the case of Windows, Microsoft Internet Information Server (IIS) is the obvious choice unless you are committed to some other package. IIS is bundled with all supported Windows Versions.
The Mascot installation program automatically configures IIS versions 8 and later.
Apache is a good choice for Linux. Apache can also be used under Windows.
Running a web browser on the same PC as the web server can take a surprising amount of processor time, so search times may suffer. If the same PC is also used for instrument control and data acquisition, you may need to adjust job priorities using Windows Task Manager to ensure that the instrument gets adequate priority.
